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convert2annovar.pl
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convert2annovar.pl
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#!/usr/bin/env perl
use warnings;
use strict;
use Getopt::Long;
use Pod::Usage;
use File::Basename;
our $REVISION = '$Revision: f98de7f0a9145baca0dd81fa66f8e3db0603abf9 $';
our $DATE = '$Date: 2019-10-24 00:05:27 -0400 (Thu, 24 Oct 2019) $';
our $AUTHOR = '$Author: Kai Wang <kaichop@gmail.com> $';
our ($verbose, $help, $man);
our ($variantfile);
our ($outfile, $format, $includeinfo, $snpqual, $snppvalue, $coverage, $maxcoverage, $chr, $chrmt, $altcov, $allelicfrac, $fraction, $species,
$filterword, $confraction, $allallele, $withzyg, $comment, $allsample, $genoqual, $varqual, $dbsnpfile, $withfreq, $withfilter, $seqdir, $inssize, $delsize, $subsize, $genefile, $splicing_threshold, $context, $avsnpfile, $keepindelref);
our %iupac = (R=>'AG', Y=>'CT', S=>'CG', W=>'AT', K=>'GT', M=>'AC', A=>'AA', C=>'CC', G=>'GG', T=>'TT', B=>'CGT', D=>'AGT', H=>'ACT', V=>'ACG', N=>'ACGT', '.'=>'-', '-'=>'-'); ### <<< FOR 5500SOLiD LifeScope ( S=>'GC' is replaced by S=>'CG')
our %iupacrev = reverse %iupac; ### <<< FOR 5500SOLiD LifeScope
GetOptions('verbose|v'=>\$verbose, 'help|h'=>\$help, 'man|m'=>\$man, 'outfile=s'=>\$outfile, 'format=s'=>\$format, 'includeinfo'=>\$includeinfo,
'snpqual=f'=>\$snpqual, 'snppvalue=f'=>\$snppvalue, 'coverage=i'=>\$coverage, 'maxcoverage=i'=>\$maxcoverage, 'chr=s'=>\$chr, 'chrmt=s'=>\$chrmt,
'fraction=f'=>\$fraction, 'altcov=i'=>\$altcov, 'allelicfrac'=>\$allelicfrac,
'species'=>\$species, 'filter=s'=>\$filterword, 'confraction=f'=>\$confraction, 'allallele!'=>\$allallele, 'withzyg'=>\$withzyg,
'comment'=>\$comment, 'allsample'=>\$allsample, 'genoqual=f'=>\$genoqual, 'varqual=f'=>\$varqual, 'dbsnpfile=s'=>\$dbsnpfile, 'withfreq'=>\$withfreq,
'withfilter'=>\$withfilter, 'seqdir=s'=>\$seqdir, 'inssize=i'=>\$inssize, 'delsize=i'=>\$delsize, 'subsize=i'=>\$subsize, 'genefile=s'=>\$genefile,
'splicing_threshold=i'=>\$splicing_threshold, 'context'=>\$context, 'avsnpfile=s'=>\$avsnpfile, 'keepindelref'=>\$keepindelref) or pod2usage ();
$help and pod2usage (-verbose=>1, -exitval=>1, -output=>\*STDOUT);
$man and pod2usage (-verbose=>2, -exitval=>1, -output=>\*STDOUT);
@ARGV or pod2usage (-verbose=>0, -exitval=>1, -output=>\*STDOUT);
@ARGV == 1 or pod2usage ("Syntax error");
($variantfile) = @ARGV;
$chrmt ||= 'M';
#prepare PATH environmental variable
my $path = File::Basename::dirname ($0);
$path and $ENV{PATH} = "$path:$ENV{PATH}"; #set up the system executable path to include the path where this program is located in
if (not $format) {
$format = 'pileup';
print STDERR "NOTICE: the default --format argument is set as 'pileup'\n";
}
$format eq 'vcf' and $format = 'vcf4';
if ($allsample) {
defined $withfreq or defined $outfile or pod2usage ("Error in argument: please specify --outfile when --allsample is specified (unless -withfreq is set)");
$format eq 'vcf4' or pod2usage ("Error in argument: the --allsample argument is supported only if --format is 'vcf4'");
defined $withfreq or print STDERR "NOTICE: output files will be written to $outfile.<samplename>.avinput\n";
} else {
if (defined $outfile) {
open (STDOUT, ">$outfile") or die "Error: cannot write to output file $outfile: $!\n";
}
}
defined $snpqual and $format eq 'pileup' || $format eq 'vcf4old' || pod2usage ("Error in argument: the --snpqual is supported only for the 'pileup' or 'vcf4old' format");
defined $snppvalue and $format eq 'gff3-solid' || pod2usage ("Error in argument: the --snppvalue is supported only for the 'gff3-solid' format");
if (not defined $snpqual and $format eq 'pileup') {
$snpqual = 20;
print STDERR "NOTICE: the default --snpqual argument for pileup format is set as 20\n";
}
if (not defined $snppvalue) {
$snppvalue = 1; #by default, do not use any of the P-value cutoff in filtering out GFF3-SOLID files (this is differnt from handling pileup files)
}
if (not defined $coverage) {
$coverage = 0;
}
if (defined $fraction) {
$format eq 'pileup' or $format eq 'vcf4' or pod2usage ("Error in argument: the '--fraction' argument is supported for the pileup or vcf4 format only");
$format eq 'vcf4old' and print STDERR "NOTICE: the --fraction argument works ONLY on indels for vcf4old format\n";
$fraction >= 0 and $fraction <=1 or pod2suage ("Error in argument: the --fraction argument must be between 0 and 1 inclusive");
} else {
$fraction = 0;
}
if (defined $withfilter) {
$format eq 'vcf4' or $format eq 'vcf4old' or pod2usage ("Error in argument: the '-withfilter' argument is supported for the vcf4 or vcf4old format only");
}
if (defined $confraction) {
$format eq 'vcf4old' and print STDERR "NOTICE: the --confraction argument works ONLY on indels for vcf4old format\n";
$confraction >= 0 and $fraction <=1 or pod2suage ("Error in argument: the --confraction argument must be between 0 and 1 inclusive");
} else {
$confraction = 0;
}
if (defined $altcov) {
$format eq 'pileup' or pod2usage ("Error in argument: the '--altcov' argument is supported for the '--format pileup' only");
$altcov < $coverage or pod2suage ("Error in argument: the --altcov argument must be less than --coverage");
$altcov > 0 or pod2suage ("Error in argument: the --altcov argument must be a positive integer");
}
if (defined $species) {
$format eq 'gff3-solid' or pod2usage ("Error in argument: the '--species' argument is only necessary for the '--format gff3-solid'");
}
if ($allallele) {
$format eq 'vcf4old' or pod2usage ("Error in argument: the '--allallele' argument is only supported for the '--format vcf4old'");
}
if ($withfreq and $withzyg) {
pod2usage ("Error in argument: -withfreq and -withzyg are mutually exclusive");
}
if ($format eq 'pileup') {
convertPileup ($variantfile);
} elsif ($format eq 'cg') {
convertCG ($variantfile);
} elsif ($format eq 'cgmastervar') {
convertCGMasterVar ($variantfile);
} elsif ($format eq 'gff3-solid') {
convertGFF3SolidSNP ($variantfile);
} elsif ($format eq 'soap') {
print STDERR "WARNING: the support for '--format soap' is not well developed yet and may contain bugs for indel analysis.\n";
convertSOAP ($variantfile);
} elsif ($format eq 'maq') {
print STDERR "WARNING: the support for '--format maq' is not well developed yet and may contain bugs.\n";
convertMAQSNP ($variantfile);
} elsif ($format eq 'casava') {
convertCASAVA ($variantfile, $chr);
} elsif ($format eq 'vcf4old') {
convertVCF4Old ($variantfile);
} elsif ($format eq 'vcf4') {
convertVCF4 ($variantfile);
} elsif ($format eq 'annovar') {
convertANNOVAR ($variantfile);
} elsif ($format eq 'annovar2vcf') {
convertANNOVAR2VCF ($variantfile);
} elsif ($format eq 'bed') {
convertBED ($variantfile);
} elsif ($format eq 'rsid') {
defined $dbsnpfile or defined $avsnpfile or pod2usage ("Error in argument: please specify --dbsnpfile or -avsnpfile when the --format is 'rsid'");
if (defined $dbsnpfile) {
convertRsid ($variantfile);
} else {
convertAvsnpid ($variantfile);
}
} elsif ($format eq 'region') {
defined $subsize or $subsize = 1;
$variantfile =~ m/(chr)?(\w+):(\d+)-(\d+)$/ or pod2usage "Error in argument: for '-format region', the region should be specified in 'chr:start-end' format";
$seqdir or pod2usage "Error in argument: please specify -seqdir for the '-format region'\n";
convertRegion ($variantfile);
} elsif ($format eq 'transcript') {
defined $subsize or $subsize = 1;
defined $genefile or pod2usage ("Error in argument; please specify -genefile for the '-format transcript'");
$seqdir or pod2usage "Error in argument: please specify -seqdir for the '-format transcript'\n";
$splicing_threshold ||= 2;
convertTranscript ($variantfile);
} else {
pod2usage ("Error in argument: the --format $format is not currently supported. Please contact ANNOVAR developer for adding the support");
}
sub convertTranscript {
my ($transcript) = @_;
my ($foundmatch) = (0);
my (@allregion);
open (GENE, $genefile) or die "Error: cannot read from gene file $genefile: $!\n";
while (<GENE>) {
s/[\r\n]+$//; #deleting the newline characters
my @record = split (/\t/, $_);
my ($name, $chr, $dbstrand, $txstart, $txend, $cdsstart, $cdsend, $exoncount, $exonstart, $exonend, $id, $name2, $cdsstartstat, $cdsendstat, $exonframes);
@record >= 11 or die "Error: invalid record in genefile (>=11 fields expected): <$_>\n";
if (@record == 12) { #knownGene
($name, $chr, $dbstrand, $txstart, $txend, $cdsstart, $cdsend, $exoncount, $exonstart, $exonend) = @record[0..9];
} else { #other gene definition
($name, $chr, $dbstrand, $txstart, $txend, $cdsstart, $cdsend, $exoncount, $exonstart, $exonend, $id, $name2, $cdsstartstat, $cdsendstat, $exonframes) = @record[1..15];
}
if ($transcript eq $name) {
$foundmatch++;
my @exonstart = split (/,/, $exonstart);
my @exonend = split (/,/, $exonend);
map {$_++} @exonstart;
for my $i (0 .. @exonstart-1) {
push @allregion, "$chr:" . ($exonstart[$i]-$splicing_threshold) . '-' . ($exonend[$i]+$splicing_threshold);
}
}
}
print STDERR "NOTICE: ${\(scalar @allregion)} regions will be analyzed for possible mutations\n";
$verbose and print STDERR "NOTICE: These regions will be analyzed: @allregion\n";
$foundmatch or print STDERR "WARNING: the specified transcript $transcript is not found in genefile $genefile\n";
$foundmatch > 1 and print STDERR "WARNING: the specified transcript $transcript occurs $foundmatch times in genefile $genefile\n";
for my $nextregion (@allregion) {
convertRegion ($nextregion);
}
}
sub convertRegion {
my ($region) = @_;
$region =~ m/(chr)?(\w+):(\d+)-(\d+)$/;
my ($chr, $start, $end) = ($2, $3, $4);
$end >= $start or die "Error: end position must be equal or larger than start position in region specification '$region'\n";
my $sc = "echo $region | retrieve_seq_from_fasta.pl -format simple -tabout -seqdir $seqdir -outfile stdout stdin";
my $result = qx/$sc/;
$result =~ m/\S+\t(\S+)/ or die "Error: unable to retrieve user-specified region $region from seqdir $seqdir\n";
my $seq = $1;
if (not defined $subsize or $subsize) { #default value is 1
my @allnt = generateAllNT ($subsize);
for my $i (0 .. length($seq)-$subsize) {
for my $nt (@allnt) {
substr($seq, $i, $subsize) eq $nt and next;
substr($seq, $i, $subsize) =~ m/^N+$/ and next; #if it is only composed of N, skip this position
print STDOUT join ("\t", $chr, $start+$i, $start+$i+$subsize-1, substr($seq, $i, $subsize), $nt), "\n";
}
}
}
if ($delsize) {
for my $i (0 .. length($seq)-$delsize) {
print STDOUT join ("\t", $chr, $start+$i, $start+$i, substr($seq, $i, $delsize), '-'), "\n";
}
}
if ($inssize) {
my @allnt = generateAllNT ($inssize);
for my $i (0 .. length($seq)-1) {
for my $nt (@allnt) {
print STDOUT join ("\t", $chr, $start+$i, $start+$i, '-', $nt), "\n";
}
}
}
}
sub generateAllNT {
my ($size) = @_;
my @oldstr = (''); #initialize as four empty string
my @newstr;
for my $i (1 .. $size) {
@newstr = ();
for my $nt (qw/A C G T/) {
for my $str (@oldstr) {
push @newstr, $str.$nt;
}
}
@oldstr = @newstr;
}
return (@newstr);
}
sub convertPileup {
my ($variantfile) = @_;
my ($countline, $countvar, $counthom, $counthet, $countindel, $countsnp, $countti, $counttv) = qw/0 0 0 0 0 0 0 0/;
if ($variantfile eq 'stdin') {
*VAR = *STDIN;
} elsif ($variantfile =~ m/\.gz$/) {
open (VAR, "gunzip -c $variantfile |") or die "Error: cannot read from STDIN uncompressing variant file $variantfile: $!\n";
} else {
open (VAR, $variantfile) or die "Error: cannot read from variant file $variantfile: $!\n";
}
print STDERR "NOTICE: Column 6-9 in output are heterozygosity status, SNP quality, total reads, reads with mutation\n";
while (<VAR>) {
s/[\r\n]+$//;
$countline++;
my $hom = 'hom';
my @field = split (/\t/, $_);
@field >= 10 or die "Error: invalid record found in pileupfile $variantfile (at least 10 fields expected): <$_>\n";
my ($chr, $pos, $wt, $call, @other) = @field;
my ($cons_qual, $snp_quality, $readcount, $readallele) = @field[4,5,7,8];
$chr =~ s/^chr//;
$wt = uc $wt; #wt may or may not in upper case, it depends on the input FASTA file
$call = uc $call; #usually call is in upper case
$readallele = uc $readallele; #lower case indicate the opposite strand
$includeinfo or @other = (); #unless -includeinfo is set, the other will not be printed
$snp_quality >= $snpqual or next; #quality of the variant call
$readcount >= $coverage or next; #read count of the variant call
$maxcoverage and $readcount <= $maxcoverage || next; #maximum coverage of the variant call
if ($wt eq '*') { #indel
#example:
#1 970271 * +C/+C 39 106 44 5 +C * 1 4 0 0 0
#1 1548977 * */+CCG 29 29 42 3 * +CCG 2 1 0 0 0
#1 1674810 * */+C 24 24 42 6 * +C 5 1 0 0 0
#1 968466 * -CT/-CT 53 339 55 5 -CT * 5 0 0 0 0
#1 1093600 * -GAAA/* 29 29 53 3 -GAAA * 1 2 0 0 0
#1 1110101 * */-A 41 41 17 6 * -A 5 1 0 0 0
#1 1215395 * */-TC 26 26 32 4 * -TC 3 1 0 0 0
my @obs = split (/\//, $call); #example: '+AG/+AG' as homozygotes, '*/-TA' or '*/+T' as heterozygotes
@obs == 2 or die "Error: pileup record contains more than two alternative alleles: <$_>\n";
my ($end, $ref, $alt);
my ($indelreadcount); #number of reads supporting the indel
if ($obs[0] eq $obs[1]) {
#something weird may occur in SamTools output: 22 15231121 * */* 360 0 32 158 * +GA 156 2 0 0 0
$obs[0] eq '*' and next;
#for deletions, SAMTOOLS represent deletion using a location before the first deleted base in the reference sequence coordinate system
#for example, a deletion in Samtools output is "1 109266688 * */-CTT 1429 1429 58 43 * -CTT 24 19 0 0 0"
#the correct ANNOVAR input (for rs35029887) should be "1 109266689 109266691 CTT - het 1429"
#insertions are fine without change; for example, check rs5745466 in Genome Browser; samtools report "1 76119508 * +AT/+AT"
#for this insertion, ANNOVAR input file (for rs5745466) becomes "1 76119508 76119508 - AT hom 1601"
if ($obs[0] =~ m/^\-/) {
$pos++; #add 1 to position in deletion
}
$indelreadcount = calculateIndelReadCount ($obs[0], \@field);
$indelreadcount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $indelreadcount >= $altcov || next;
if ($chr eq $chrmt or $allelicfrac) {
$hom = sprintf ("%.3f", $indelreadcount/$readcount);
}
($end, $ref, $alt) = recalculateEndRefObs ($pos, $wt, $obs[0]);
print STDOUT join ("\t", $chr, $pos, $end, $ref, $alt, $hom, $snp_quality, $readcount, $indelreadcount, @other), "\n";
$counthom++;
} else {
$hom = 'het';
if ($obs[0] =~ m/^[\-\+]/) {
$obs[0] =~ m/^\-/ and $pos++;
($end, $ref, $alt) = recalculateEndRefObs ($pos, $wt, $obs[0]);
$indelreadcount = calculateIndelReadCount ($obs[0], \@field);
$indelreadcount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $indelreadcount >= $altcov || next;
if ($chr eq $chrmt or $allelicfrac) {
$hom = sprintf ("%.3f", $indelreadcount/$readcount);
}
print STDOUT join ("\t", $chr, $pos, $end, $ref, $alt, $hom, $snp_quality, $readcount, $indelreadcount, @other), "\n";
$counthet++;
}
if ($obs[1] =~ m/^[\-\+]/) {
$obs[1] =~ m/^\-/ and $pos++;
($end, $ref, $alt) = recalculateEndRefObs ($pos, $wt, $obs[1]);
$indelreadcount = calculateIndelReadCount ($obs[1], \@field);
$indelreadcount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $indelreadcount >= $altcov || next;
if ($chr eq $chrmt or $allelicfrac) {
$hom = sprintf ("%.3f", $indelreadcount/$readcount);
}
print STDOUT join ("\t", $chr, $pos, $end, $ref, $alt, $hom, $snp_quality, $readcount, $indelreadcount, @other), "\n";
$counthet++;
}
}
$countindel++;
} else {
#1 798494 G A 36 36 58 3 AAA bbb
#1 798677 T K 33 33 52 26 ,$.,,G.GG,.,......,..G,,... b`bbBaJIbFbZWaTNQbb_VZcbbb
#1 856182 G A 42 42 50 5 AAAAA B\bbb
#1 861034 A M 48 48 49 14 ,$,.,..,cc.c.,c bbBbb`]BFbHbBB
#1 864289 T K 22 22 56 6 .g,,g, BH^_BB
$wt eq $call and next; #this is not a SNP
my $obs = $iupac{$call} or die "Error: invalid best call ($call) in <$_>\n";
my @obs = split (//, $obs);
@obs == 2 or die "Error: observed IUPAC allele $call should correspond to two nucleotide alleles: <$_>\n";
if ($obs[0] ne $obs[1]) {
$hom = 'het';
}
if ($obs[0] eq $wt) { #obs[0] is guaranteed to be an alternative allele
@obs = @obs[1,0];
}
if ($wt eq 'A' and $obs[0] eq 'G' or $wt eq 'G' and $obs[0] eq 'A' or $wt eq 'C' and $obs[0] eq 'T' or $wt eq 'T' and $obs[0] eq 'C') {
unless ($wt ne $obs[0] and $wt ne $obs[1] and $obs[0] ne $obs[1]) {
$countti++;
}
} else {
unless ($wt ne $obs[0] and $wt ne $obs[1] and $obs[0] ne $obs[1]) {
$counttv++;
}
}
my $mutallelecount;
if ($obs[1] eq $wt) { #het SNP
if ($chr eq $chrmt or $allelicfrac) {
$hom = calculateAllelicFraction ($obs[0], $field[8], $readcount);
}
$mutallelecount = calculateMutAlleleCount ($obs[0], $readallele);
$mutallelecount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $mutallelecount >= $altcov || next;
print STDOUT join ("\t", $chr, $pos, $pos, $wt, $obs[0], $hom, $snp_quality, $readcount, $mutallelecount, @other), "\n";
$counthet++;
} elsif ($obs[1] ne $obs[0]) { #het SNP but both differ from reference allele
if ($chr eq $chrmt or $allelicfrac) {
$hom = calculateAllelicFraction ($obs[1], $field[8], $readcount);
}
$mutallelecount = calculateMutAlleleCount ($obs[1], $readallele);
$mutallelecount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $mutallelecount >= $altcov || next;
print STDOUT join ("\t", $chr, $pos, $pos, $wt, $obs[1], $hom, $snp_quality, $readcount, $mutallelecount, @other), "\n";
if ($chr eq $chrmt) {
$hom = calculateAllelicFraction ($obs[0], $field[8], $readcount);
}
$mutallelecount = calculateMutAlleleCount ($obs[0], $readallele);
$mutallelecount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $mutallelecount >= $altcov || next;
print STDOUT join ("\t", $chr, $pos, $pos, $wt, $obs[0], $hom, $snp_quality, $readcount, $mutallelecount, @other), "\n";
$counthet++;
$counthet++;
} else { #homo SNP
if ($chr eq $chrmt or $allelicfrac) {
$hom = calculateAllelicFraction ($obs[0], $field[8], $readcount);
}
$mutallelecount = calculateMutAlleleCount ($obs[0], $readallele);
$mutallelecount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $mutallelecount >= $altcov || next;
print STDOUT join ("\t", $chr, $pos, $pos, $wt, $obs[0], $hom, $snp_quality, $readcount, $mutallelecount, @other), "\n";
$counthom++;
}
$countsnp++;
}
$countvar++;
}
my $triallelic = $countsnp-$countti-$counttv;
print STDERR "NOTICE: Read $countline lines and wrote ${\($counthet+$counthom)} different variants at $countvar genomic positions ($countsnp SNPs and $countindel indels)\n";
print STDERR "NOTICE: Among ${\($counthet+$counthom)} different variants at $countvar positions, $counthet are heterozygotes, $counthom are homozygotes\n";
print STDERR "NOTICE: Among $countsnp SNPs, $countti are transitions, $counttv are transversions", $triallelic?", $triallelic have more than 2 alleles\n":"\n";
}
sub calculateIndelReadCount {
my ($obs, $field) = @_;
#make sure to use upper case in the comparison, for example:
#chr10 130133 * */-ca 189 189 59 31 * -ca 27 4 0 0 0
if ($obs eq uc $field->[8]) {
return $field->[10];
} elsif ($obs eq uc $field->[9]) {
return $field->[11];
} else {
die "Error: invalid record in pileup file (indel counts cannot be inferred): <$obs> vs <@$field>\n";
}
}
sub calculateMutAlleleCount {
my ($allele, $string) = @_; #they should be already both in upper case
$string =~ s/\^.//g; #^ is followed by mapping quality
$string =~ s/\$//g;
$string =~ s/[+-]1[^\d]//g; #1 followed by a non-number
$string =~ s/[+-]2..//g;
$string =~ s/[+-]3...//g;
$string =~ s/[+-]4....//g;
$string =~ s/[+-]5.....//g;
$string =~ s/[+-]6......//g;
$string =~ s/[+-]7.......//g;
$string =~ s/[+-]8........//g;
$string =~ s/[+-]9.........//g;
$string =~ s/[+-]10..........//g;
#make sure to use upper case letter
my @string = split (//, uc $string);
my $count = 0;
for my $i (0 .. @string-1) {
$allele eq $string[$i] and $count++;
}
return $count;
}
sub calculateAllelicFraction {
my ($obs, $readbase, $readcount) = @_;
my @readbase = split (//, $readbase);
my $count=0;
for my $i (0 .. @readbase-1) {
uc $obs eq uc $readbase[$i] and $count++;
}
my $hom = $count/$readcount;
length ($hom) > 5 and $hom > 0.001 and $hom = sprintf ("%.3f", $hom);
return $hom;
}
sub recalculateEndRefObs { #recalculate end position, reference allele and observed allele
my ($end, $ref, $obs) = @_;
if ($obs =~ m/^\-(\w+)/) { #deletion
$end += (length ($1)-1);
$ref = $1;
$obs = '-';
} elsif ($obs =~ m/^\+(\w+)/) { #insertion
$ref = '-';
$obs = $1;
} else {
die "Error: cannot handle $end, $ref, $obs\n";
}
return ($end, $ref, $obs);
}
sub convertBED {
my ($variantfile) = @_;
my ($foundheader, $countline, $countvar) = qw/0 0 0/;
my ($prechr, $prestart, $preend, $prevartype, $preref, $preobs, $prescore, $prexref) = qw/0 0 0 0 0 0 0 0/;
if ($variantfile eq 'stdin') {
*VAR = *STDIN;
} elsif ($variantfile =~ m/\.gz$/) {
open (VAR, "gunzip -c $variantfile |") or die "Error: cannot read from STDIN uncompressing variant file $variantfile: $!\n";
} else {
open (VAR, $variantfile) or die "Error: cannot read from variant file $variantfile: $!\n";
}
print STDERR "NOTICE: Converting variants from $variantfile\n";
while (<VAR>) {
s/[\r\n]+$//;
$countline++;
m/^#/ and next; #comment lines
if (m/^track/) {
$foundheader++;
next;
}
if (not $foundheader) {
$countline > 10 and die "Error: invalid BED file format for $variantfile (track record is not found within the first 10 lines)\n";
}
my ($chrom, $start, $end, @otherinfo) = split (/\t/, $_);
$chrom =~ s/^chr//;
print join ("\t", $chrom, $start+1, $end, 0, 0, @otherinfo), "\n";
$countvar++;
}
print STDERR "NOTICE: Done with $countline lines and $countvar variants\n";
}
sub convertCG {
my ($variantfile) = @_;
my ($foundheader, $countline, @field);
my ($prechr, $prestart, $preend, $prevartype, $preref, $preobs, $prescore, $prexref) = qw/0 0 0 0 0 0 0 0/;
if ($variantfile eq 'stdin') {
*VAR = *STDIN;
} elsif ($variantfile =~ m/\.gz$/) {
open (VAR, "gunzip -c $variantfile |") or die "Error: cannot read from STDIN uncompressing variant file $variantfile: $!\n";
} else {
open (VAR, $variantfile) or die "Error: cannot read from variant file $variantfile: $!\n";
}
print STDERR "NOTICE: Converting variants from $variantfile\n";
while (<VAR>) {
s/[\r\n]+$//;
$countline++;
if (m/^>locus/) {
$foundheader++;
}
if (not $foundheader) {
$countline > 50 and die "Error: invalid CG-var file format for $variantfile (>locus record is not found within the first 50 lines)\n";
next;
}
my ($locus, $ploidy, $haplo, $chr, $start, $end, $vartype, $ref, $obs, $score, $haplolink, $xref) = split (/\t/, $_);
$chr =~ s/^chr//;
$vartype eq 'ins' or $start++; #CG use zero-start, half-open coordinate. Insertion does not need to be processed (example, "16476 2 2 chr1 751820 751820 ins T 49 dbsnp:rs59038458")
$obs eq '' and $obs = '-';
$ref eq '' and $ref = '-';
if ($vartype =~ m/^snp|ins|del|delins|sub$/) { #in new versions of the files, "sub" is used instead of "delins".
#$chr eq 'M' and next; #ignore chrM markers as they are not diploid
if ($chr eq $prechr and $start eq $prestart and $end eq $preend and $obs eq $preobs) { #homozygous mutation
print $chr, "\t", $start, "\t", $end, "\t", $ref, "\t", $obs, "\t", $vartype, "\t", ($score+$prescore)/2, "\t", "hom\t", $xref, "\n";
($prechr, $prestart, $preend, $prevartype, $preref, $preobs, $prescore, $prexref) = qw/0 0 0 0 0 0 0 0/;
} else {
if ($prestart and $preend) {
print $prechr, "\t", $prestart, "\t", $preend, "\t", $preref, "\t", $preobs, "\t", $prevartype, "\t", $prescore, "\thet\t", $prexref, "\n";
}
($prechr, $prestart, $preend, $prevartype, $preref, $preobs, $prescore, $prexref) = ($chr, $start, $end, $vartype, $ref, $obs, $score, $xref);
}
}
}
if ($prestart and $preend) {
print $prechr, "\t", $prestart, "\t", $preend, "\t", $preref, "\t", $preobs, "\t", $prevartype, "\t", $prescore, "\thet\t", $prexref, "\n";
}
print STDERR "NOTICE: Done with $countline lines\n";
}
sub convertCGMasterVar {
#this subroutine converts CG masterVar format into ANNOVAR input format
#example input file is below:
#SEGDUP_GENERATED_AT 2010-Dec-01 13:40
#SOFTWARE_VERSION 2.0.2.26
#TYPE VAR-OLPL
#>locus ploidy chromosome begin end zygosity varType reference allele1Seq allele2Seq allele1VarScoreVAF allele2VarScoreVAF allele1VarScoreEAF allele2VarScoreEAF allele1VarQuality allele2VarQuality allele1HapLink allele2HapLink allele1XRef allele2XRef evidenceIntervalId allele1ReadCount allele2ReadCount referenceAlleleReadCount totalReadCount allele1Gene allele2Gene pfam miRBaseId repeatMasker segDupOverlap relativeCoverageDiploid calledPloidy relativeCoverageNondiploid calledLevel
#1 2 chr1 0 10000 no-call no-ref = ? ?
#2 2 chr1 10000 11038 no-call complex = ? ? 1.13 N 1.02 1.006
#3 2 chr1 11038 11055 hom ref = = = 1.13 N 1.02 1.006
#4 2 chr1 11055 11082 no-call complex = ? ? 1.13 N 1.02 1.006
#5 2 chr1 11082 11109 hom ref = = = 1.13 N 1.02 1.006
my ($variantfile) = @_;
my ($foundheader, $countline);
if ($variantfile eq 'stdin') {
*VAR = *STDIN;
} elsif ($variantfile =~ m/\.gz$/) {
open (VAR, "gunzip -c $variantfile |") or die "Error: cannot read from STDIN uncompressing variant file $variantfile: $!\n";
} else {
open (VAR, $variantfile) or die "Error: cannot read from variant file $variantfile: $!\n";
}
print STDERR "NOTICE: Converting variants from $variantfile\n";
while (<VAR>) {
s/[\r\n]+$//;
$countline++;
if (m/^>locus/) {
$foundheader++;
}
if (not $foundheader) {
$countline > 50 and die "Error: invalid CG-var file format for $variantfile (>locus record is not found within the first 50 lines)\n";
next;
}
my ($locus, $ploidy, $chr, $start, $end, $zygosity, $vartype, $ref, $obs1, $obs2, @otherinfo) = split (/\t/, $_, -1);
my ($a1scorevaf, $a2scorevaf, $a1scoreeaf, $a2scoreeaf, $a1varqual, $a2varqual, $a1haplink, $a2haplink, $a1xref, $a2xref, $interval, $a1read, $a2read, $refread, $totalread) = @otherinfo;
$chr =~ s/^chr//;
$vartype eq 'ins' or $start++; #CG use zero-start, half-open coordinate. Insertion does not need to be processed (example, "16476 2 2 chr1 751820 751820 ins T 49 dbsnp:rs59038458")
$obs1 eq '' and $obs1 = '-';
$obs2 eq '' and $obs2 = '-';
$ref eq '' and $ref = '-';
#zygosity explanation:
##no-call: All alleles are partially or fully no-called.
##hap: Haploid, fully called locus.
##half: Diploid locus where one of the alleles is fully called and the other contains no-calls.
##hom: Diploid, homozygous, fully called locus.
##het-ref: Diploid, heterozygous, fully called locus where one of the alleles is identical to the reference.
##het-alt: Diploid, heterozygous, fully called locus where both alleles differ from the reference.
#vartype explanation:
##snp, ins, del, or sub: Fully called or half-called locus that contains only a single isolated variation.
##ref: Fully called or half-called locus that contains only reference calls and no calls and at least one allele is fully called.
##complex: Locus that contains multiple variations or has no-calls in all alleles. This is also the value for all loci where the reference itself is ambiguous.
##no-ref: Locus where the reference genome is N.
##PAR-called-in-X: Locus on the pseudo-autosomal region of the Y chromosomes in males.
$zygosity eq 'no-call' and next; #ignore locus without calls
if ($vartype =~ m/^snp|ins|del|delins|sub$/) { #in new versions of the files, "sub" is used instead of "delins".
if ($coverage) {
$totalread >= $coverage or next;
}
if ($maxcoverage) {
$totalread <= $maxcoverage or next;
}
if ($zygosity eq 'hom' or $zygosity eq 'hap') {
print $chr, "\t", $start, "\t", $end, "\t", $ref, "\t", $obs1, "\t", 'hom', "\t", $vartype, "\t", $totalread, "\t", $includeinfo?join("\t", "\t", @otherinfo):'', "\n";
} else {
print $chr, "\t", $start, "\t", $end, "\t", $ref, "\t", $obs1, "\t", 'het', "\t", $vartype, "\t", $totalread, "\t", $includeinfo?join("\t", "\t", @otherinfo):'', "\n";
}
}
}
print STDERR "NOTICE: Done with $countline lines\n";
}
sub convertGFF3SolidSNP {
my ($variantfile) = @_;
my ($countline, $countvar, $countallvar, @other) = (0, 0, 0);
my ($unknown_count); #count of variants with 'unknown' variation type
if ($variantfile eq 'stdin') {
*VAR = *STDIN;
} elsif ($variantfile =~ m/\.gz$/) {
open (VAR, "gunzip -c $variantfile |") or die "Error: cannot read from STDIN uncompressing variant file $variantfile: $!\n";
} else {
open (VAR, $variantfile) or die "Error: cannot read from variant file $variantfile: $!\n";
}
$_ = <VAR>;
s/[\r\n]+$//;
m/^##gff-version\s+3/ or die "Error: invalid first line in GFF3 file ('##gff-version 3' expected): <$_>\n";
$_ = <VAR>;
s/[\r\n]+$//;
(m/^##solid-gff-version/ || m/^##source-version/) or print STDERR "WARNING: problematic second line in GFF3-SOLiD file ('##solid-gff-version' or '##source-version' expected): <$_>\n"; ### <<< FOR 5500SOLiD LifeScope
print STDERR "NOTICE: Column 6-9 in output are heterozygosity status, variant score (P-value), total clipped normal coverage reads, total reads with mutated allele\n";
while (<VAR>) {
s/[\r\n]+$//;
$countline++;
if ($comment) {
m/^#/ and print and next; #keep comment in output file
} else {
m/^##/ and next; #header of comment lines
m/^#/ and next; #header of results lines
}
my @field = split (/\t/, $_);
@field == 9 or die "Error: invalid record found in $variantfile (10 fields expected): <$_>\n";
my ($chr, $program, $type, $pos, $end, $score, $attribute) = @field[0,1,2,3,4,5,8]; #score is the P-value for the SNP calls
$chr eq 'chr_name' and next; #header line
if ($score ne '.') {
$score >=0 and $score <=1 or die "Error: invalid score record found in file (0-1 range expected): <$_>\n";
$score <= $snppvalue or next;
}
if ($species and $species eq 'human') {
$chr eq '23' and $chr = 'X';
$chr eq '24' and $chr = 'Y';
$chr eq '25' and $chr = 'M';
}
$includeinfo and @other = ($attribute); #unless -includeinfo is set, the other will not be printed
my ($readcount, $mutallelecount) = ('.', '.'); #total coverage, coverage for mutated alleles
if ($type eq 'unknown') {
#SOLiD GDD3 may have unknown variation types
#chr1 AB_SOLiD Small Indel Tool unknown 3833062 3833153 1 . . ID=5483;len=no_call;allele-call-pos=3833062;allele-call=/CCAC;allele-pos=3833057;alleles=atccatccacccatc/aTCCATCCACCCACCCATC/NO_CALL;allele-counts=REF,2,2;tight_chrom_pos=none;loose_chrom_pos=3833058-3833069;no_nonred_reads=3;coverage_ratio=8.0000;experimental-zygosity=HEMIZYGOUS;experimental-zygosity-score=1.0000;run_names=L1_1_50_10_r,L1_1_50_15_r,L1_1_50_15_r,L1_1_50_12_r;bead_ids=1018_196_970,699_1263_465,220_513_923,2022_1532_1071;overall_qvs=4,6,2,50;no_mismatches=5,4,2,0;read_pos=27,29,31,13;from_end_pos=23,21,19,37;strands=+,+,+,+;tags=R3,F3,F3,F3;indel_sizes=-92,-112,4,4;non_indel_no_mismatches=0,0,8,0;unmatched-lengths=50,50,50,50;ave-unmatched=50.0000;anchor-match-lengths=48,49,49,49;ave-anchor-length=48.7500;read_seqs=G23223321322112233223100132013201320110011001322332,T33223321322112233223100132013201320110013021322332,T33223321322112233223100132013201320110011001322332,T31001320132013201100110013223322113030332233113032;base_qvs=;non_indel_seqs=T21322332211221121322332230321212121223322332233221,G12020202202020012001200213022002130012332310122030,G12020202202020012001000210022012110312331331122030,G22111012101031010100002002321020002202121121313021;non_indel_qvs=
$unknown_count++;
next; #do not count this one!
}
if ($program eq 'SOLiD_diBayes' or $program eq 'AB_SOLiD SNP caller') { #SNP variants
#detailed description can be found at http://solidsoftwaretools.com/gf/download/docmanfileversion/208/866/DiBayes_Documentation_v1.2.pdf
#chr1 SOLiD_diBayes SNP 559817 559817 0.094413 . . genotype=Y;reference=T;coverage=9;refAlleleCounts=5;refAlleleStarts=4;refAlleleMeanQV=23;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=14;diColor1=11;diColor2=33;het=1;flag=
#chr1 SOLiD_diBayes SNP 714068 714068 0.000000 . . genotype=M;reference=C;coverage=13;refAlleleCounts=7;refAlleleStarts=6;refAlleleMeanQV=25;novelAlleleCounts=6;novelAlleleStarts=4;novelAlleleMeanQV=22;diColor1=00;diColor2=11;het=1;flag=
#chr1 SOLiD_diBayes SNP 714835 714835 0.041579 . . genotype=R;reference=A;coverage=5;refAlleleCounts=3;refAlleleStarts=3;refAlleleMeanQV=18;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=20;diColor1=02;diColor2=20;het=1;flag=
$pos == $end or die "Error: invalid record found in GFF3-SOLiD file: start and end discordant: <$_>\n";
my ($wt, $call);
my ($hit); ### <<< FOR 5500SOLiD LifeScope
if ($attribute =~ m/ref_base=(\w)/) {
$wt = $1;
} elsif ($attribute =~ m/reference=(\w)/) {
$wt = $1;
} else {
die "Error: invalid record found in GFF3-SOLiD file (ref_base/reference was not found): <$_>\n";
}
if ($attribute =~ m/consen_base=(\w)/) {
$call = $1;
} elsif ($attribute =~ m/genotype=(\w)/) {
$call = $1;
} elsif ($attribute =~ m/allele-call=([\w\/]+)/) { ### <<< FOR 5500SOLiD LifeScope
$hit = $1;
if ($hit =~ m/\//) {
$call = $iupacrev{join("",sort(split(/\//,$hit)))};
} else {
$call = $hit;
}
} else {
die "Error: invalid record found in GFF3-SOLiD file (consen_base was not found): <$_>\n";
}
if ($attribute =~ m/coverage=(\d+)/) {
$readcount = $1;
$readcount >= $coverage or next; #read count of the variant call
$maxcoverage and $readcount <= $maxcoverage || next;
}
if ($attribute =~ m/novelAlleleCounts=(\d+)/) {
$mutallelecount = $1;
$mutallelecount/$readcount >= $fraction or next; #do not meet minimum alternative allele fraction threshold
defined $altcov and $mutallelecount >= $altcov || next;
}
my $obs = $iupac{$call} or die "Error: invalid best call in <$_>\n";
my @obs = split (//, $obs);
@obs == 2 or die "Error: observed IUPAC allele $call should correspond to two nucleotide alleles: <$_>\n";
if ($obs[0] eq $wt and $obs[1] eq $wt) {
die "Error: reference alleles are identical to observed alleles: <$_>\n";
} elsif ($obs[0] eq $wt) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[1], "\t", "het\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
} elsif ($obs[1] eq $wt) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "het\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
} elsif ($obs[1] ne $obs[0]) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "het\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[1], "\t", "het\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
$countallvar++;
} else {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "hom\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
}
} elsif ($program eq 'AB_CNV_PIPELINE') { #CNV
if ($attribute =~ m/copynum=(\d+)/ or $attribute =~ m/copynumber=(\d+)/) {
if ($1 < 2) {
print $chr, "\t", $pos, "\t", $end, "\t", 0, "\t", '-', "\t", "unk\t", "$score\t.\t.\t", join ("\t", @other), "\n";
} elsif ($1 > 2) {
print $chr, "\t", $end, "\t", $end, "\t", '-', "\t", 0, "\t", "unk\t", "$score\t.\t.\t", join ("\t", @other), "\n";
}
} else {
print $chr, "\t", $end, "\t", $end, "\t", '-', "\t", 0, "\t", "unk\t", "$score\t.\t.\t", join ("\t", @other), "\n";
}
} elsif ($program eq 'AB_SOLiD Large Indel Tool') { #CNV
#http://solidsoftwaretools.com/gf/download/docmanfileversion/182/780/Large_Indel_Documentation_v1.0.0.pdf
## [FIELDS] (1) chromosome (2) version (3) indel type (4) breakpoint start (5) breakpoint end (6) p-value (7) NA (8) NA (9) attributes
#chr10 AB_SOLiD Large Indel Tool insertion 151910 151969 2.77548e-11 . . dev=-71;avgDev=-1.63884;zygosity=HOMOZYGOUS;nRef=0;nDev=14;refDev=0;devDev=-1.60924;refVar=0;devVar=0.0159438;beadIds=1750_720_1641,649_1680_794,503_1756_608,1726_174_1362,1208_1772_353,872_594_1604,1924_990_858,1899_961_1848,901_1226_378,323_1750_1017,1185_180_1237,1519_490_1074,1291_94_324,285_758_922,1135_95_1594,1055_218_1279,
#chr10 AB_SOLiD Large Indel Tool insertion 154109 154729 2.1559e-11 . . dev=-66;avgDev=-1.51253;zygosity=HOMOZYGOUS;nRef=0;nDev=15;refDev=0;devDev=-1.02864;refVar=0;devVar=0.133236;beadIds=1728_1671_1739,1250_231_25,811_783_1090,1035_908_491,649_1680_794,503_1756_608,1726_174_1362,1208_1772_353,872_594_1604,1924_990_858,1899_961_1848,901_1226_378,323_1750_1017,1185_180_1237,1519_490_1074,1291_94_324,285_758_922,1135_95_1594,1055_218_1279,
my ($call, @call, $zygosity);
if ($attribute =~ m#zygosity=HEMIZYGOUS#) {
$zygosity = 'het';
} elsif ($attribute =~ m#zygosity=HOMOZYGOUS#) {
$zygosity = 'hom';
} else {
$zygosity = 'unk';
}
if ($type eq 'insertion') {
#the true boundary is unknown (start is different from end) so we cannot use "-" to represent reference allele.
print $chr, "\t", $pos, "\t", $end, "\t", 0, "\t", 0, "\t", $zygosity, "\t", "$score\t.\t.\t", join ("\t", @other), "\n";
} elsif ($type eq 'deletion') {
print $chr, "\t", $pos, "\t", $end, "\t", 0, "\t", '-', "\t", $zygosity, "\t", "$score\t.\t.\t", join ("\t", @other), "\n";
}
} elsif ($program eq 'AB_SOLiD Small Indel Tool') { #small indels
#typical simple insertion and deletions
#chr1 AB_SOLiD Small Indel Tool deletion 1352612 1352614 1 . . ID=1290;del_len=3;allele-call-pos=1352612;allele-call=cct/;allele-pos=1352610;alleles=cccctccat/cCCCAT;allele-counts=REF,2;tight_chrom_pos=1352612-1352614;loose_chrom_pos=1352612-1352614;no_nonred_reads=2;coverage_ratio=11.5000;experimental-zygosity=HEMIZYGOUS;experimental-zygosity-score=1.0000;run_names=L1_1_25_3_r,L1_1_25_8_r;bead_ids=1470_2000_506,822_1710_1767;overall_qvs=18,19;no_mismatches=3,3;read_pos=6,13;from_end_pos=19,12;strands=-,+;tags=R3,R3;indel_sizes=-3,-3;non_indel_no_mismatches=1,-1;unmatched-lengths=25,25;ave-unmatched=25.0000;anchor-match-lengths=24,99;ave-anchor-length=61.5000;read_seqs=G0112310001100003120031200,G0300213000011000132110021;base_qvs=;non_indel_seqs=T2120033002022200220000002,;non_indel_qvs=
#chr1 AB_SOLiD Small Indel Tool insertion_site 1311162 1311162 1 . . ID=1249;ins_len=1;allele-call-pos=1311162;allele-call=/G;allele-pos=1311161;alleles=gaggggggg/GAGGGGGGGG/NO_CALL;allele-counts=REF,3,1;tight_chrom_pos=none;loose_chrom_pos=1311160-1311169;no_nonred_reads=3;coverage_ratio=4.6667;experimental-zygosity=HEMIZYGOUS;experimental-zygosity-score=1.0000;run_names=L1_1_25_6_r,L1_1_50_10_r,L1_1_25_2_r,L1_1_25_3_r;bead_ids=850_837_429,1160_878_181,404_1050_1881,1084_64_1343;overall_qvs=20,56,25,25;no_mismatches=3,2,2,1;read_pos=11,22,11,11;from_end_pos=14,28,14,14;strands=+,-,-,-;tags=R3,F3,F3,F3;indel_sizes=1,1,1,1;non_indel_no_mismatches=-1,1,0,1;unmatched-lengths=25,50,25,25;ave-unmatched=31.2500;anchor-match-lengths=99,49,24,24;ave-anchor-length=49.0000;read_seqs=G1020001130221020000000020,T03223323210110021000000022122030100020221222222122,T0102210000000221223301000,T0102210000000221220301000;base_qvs=;non_indel_seqs=,G21202030032202013220021321131212021000122300013132,G1331133120001221220120120,G1331133120001221220120220;non_indel_qvs=
#sometimes, allele-call is ambiguous that requires a "block substitution" representation (although they were annotated as insertion or deletion by SOLiD, they should be treated as block substitution by ANNOVAR)
#sometimes, mutiple allele calls may be present at the same site
#chr1 AB_SOLiD Small Indel Tool deletion 1209357 1209360 1 . . ID=1101;del_len=4;allele-call-pos=1209357;allele-call=ggtggg/TT;allele-pos=1209355;alleles=ggggtgggggggtt/gGTTGGGGTT/gGTGTTTTGCCTT/NO_CALL;allele-counts=REF,3,1,1;tight_chrom_pos=none;loose_chrom_pos=1209357-1209363;no_nonred_reads=4;coverage_ratio=3.0000;experimental-zygosity=HEMIZYGOUS;experimental-zygosity-score=0.9888;run_names=L1_1_25_1_r,L1_1_25_2_r,L1_1_25_4_r,L1_1_25_3_r,L1_1_25_7_r;bead_ids=1017_1024_53,1493_1896_615,1794_647_1473,307_1116_687,773_1492_1671;overall_qvs=24,24,28,24,8;no_mismatches=2,3,2,3,2;read_pos=14,9,14,9,15;from_end_pos=11,16,11,16,10;strands=-,+,-,+,+;tags=F3,R3,F3,F3,F3;indel_sizes=-4,-4,-4,-4,3;non_indel_no_mismatches=1,0,0,0,0;unmatched-lengths=25,25,25,25,25;ave-unmatched=25.0000;anchor-match-lengths=24,24,24,24,24;ave-anchor-length=24.0000;read_seqs=T2221100101000101000221100,G0001122000100000101001020,T2221100101000101000221100,T1112200010100010100112000,T1011220000111000130200001;base_qvs=;non_indel_seqs=G0312033221312111022200300,T0111113210210112100001130,G0312133221312111022200300,G0231003132222112000012020,G3121331033101113122312020;non_indel_qvs=
#chr1 AB_SOLiD Small Indel Tool deletion 1209436 1209436 1 . . ID=1103;del_len=1;allele-call-pos=1209436;allele-call=ag/A/G;allele-pos=1209434;alleles=tgagggggtt/tGAGGGGTT/tGGGGGGTT;allele-counts=REF,1,1;tight_chrom_pos=none;loose_chrom_pos=1209436-1209441;no_nonred_reads=2;coverage_ratio=5.0000;experimental-zygosity=HEMIZYGOUS;experimental-zygosity-score=1.0000;run_names=L1_1_25_6_r,L1_1_25_2_r;bead_ids=1315_1584_2005,1706_194_437;overall_qvs=28,21;no_mismatches=0,3;read_pos=9,7;from_end_pos=16,18;strands=-,-;tags=R3,R3;indel_sizes=-1,-1;non_indel_no_mismatches=-1,0;unmatched-lengths=25,25;ave-unmatched=25.0000;anchor-match-lengths=99,24;ave-anchor-length=61.5000;read_seqs=G3001010000011001010000001,G3010100022110010111000110;base_qvs=;non_indel_seqs=,T1112003220020013202122300;non_indel_qvs=
#chr1 AB_SOLiD Small Indel Tool insertion_site 1424540 1424540 1 . . ID=1376;ins_len=3;allele-call-pos=1424540;allele-call=tt/CCCAC;allele-pos=1424537;alleles=ttttttg/TTTCCCACTG/NO_CALL;allele-counts=REF,1,1;tight_chrom_pos=none;loose_chrom_pos=1424536-1424543;no_nonred_reads=2;coverage_ratio=11.5000;experimental-zygosity=HEMIZYGOUS;experimental-zygosity-score=1.0000;run_names=L1_1_25_7_r,L1_1_50_16_r;bead_ids=703_437_370,1089_878_1744;overall_qvs=1,9;no_mismatches=3,4;read_pos=5,35;from_end_pos=20,15;strands=-,-;tags=R3,F3;indel_sizes=3,3;non_indel_no_mismatches=2,0;unmatched-lengths=25,50;ave-unmatched=37.5000;anchor-match-lengths=24,47;ave-anchor-length=35.5000;read_seqs=G2032002200200000000000020,T30100102220312202103112130230322210121100200002100;base_qvs=;non_indel_seqs=T2121120003012303000000000,G22213300221101011121030022002222300220322213303102;non_indel_qvs=
my ($call, @call, $zygosity);
my ($refcall, $gapnonred, %temphash); ### <<< FOR 5500SOLiD LifeScope
#if ($attribute =~ m#experimental-zygosity=HEMIZYGOUS# ||$attribute =~ m#zygosity=HEMIZYGOUS#) { ### <<< FOR 5500SOLiD LifeScope
# $zygosity = 'het';
#} elsif ($attribute =~ m#experimental-zygosity=HOMOZYGOUS# || $attribute =~ m#zygosity=HOMOZYGOUS#) { ### <<< FOR 5500SOLiD LifeScope
#the above 3 lines are replaced by the following 3 lines on 20120618
if ($attribute =~ m#zygosity=(MULTI-)?HEMIZYGOUS#) { ### <<< FOR 5500SOLiD LifeScope
$zygosity = 'het';
} elsif ($attribute =~ m#zygosity=(MULTI-)?HOMOZYGOUS#) { ### <<< FOR 5500SOLiD LifeScope
$zygosity = 'hom';
} else {
$zygosity = 'unk';
}
$score = '.'; #by default, score=1 in the output
#no_nonred_reads: Number of reads with unique start positions (non-redundant reads).
#coverage_ratio: Clipped normal coverage/number of non-redundant reads.Clipped coverage is where the parts of the read that are within 5 bp at either end are not counted as a part of coverage.
if ($attribute =~ m/no_nonred_reads=(\d+);coverage_ratio=([\d\.]+)/) {
$readcount = int ($1*$2);
$readcount >= $coverage or next; #clipped normal read count of the variant call (this could even be lower than mut allele count)
$maxcoverage and $readcount <= $maxcoverage || next;
} elsif ($attribute =~ m/gap-nonred-reads=(\d+)/) { ### <<< FOR 5500SOLiD LifeScope
$gapnonred = $1;
$attribute =~ m/coverage_ratio=(\d+)/;
$readcount = int($gapnonred*$1);
$readcount >= $coverage or next;
$maxcoverage and $readcount <= $maxcoverage || next;
} else {
$readcount = '.';
}
if ($attribute =~ m/allele-counts=REF,(\d+)/) {
$mutallelecount = $1;
} elsif ($attribute =~ m/context-variant-reads=(\d+)/) { ### <<< FOR 5500SOLiD LifeScope
$mutallelecount = $1;
}
if ($attribute =~ m#reference=([\w\-]+)#) { ### <<< FOR 5500SOLiD LifeScope (using "reference" tag for the reference allele)
$refcall = $1;
$attribute =~ m#;allele\-call=([\w\-\/]+)#;
foreach my $item(split(/\//, $1)) { $temphash{$item}++; } # collecting unique alleles
delete $temphash{"possibleOthers"}; # ingore the "possibleOthers" allele
@call = keys %temphash;
if ($1 eq '-/-') { # a simple deletion ["allele-call=-/-"] (for the end position, "$end" is already not used)
print $chr, "\t", $pos, "\t", $pos+length($refcall)-1, "\t", $refcall, "\t", '-', "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
} elsif ($refcall eq '-') { # a simple insertion (single or multiple allele) ["reference=-"]
for my $i (0 .. @call-1) {
next if ($refcall eq $call[$i]);
print $chr, "\t", $pos, "\t", $pos, "\t", '-', "\t", $call[$i], "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
$i > 0 and $countallvar++;
}
} else { # an indel that may have several alleles, or may require a block substitution representation
for my $i (0 .. @call-1) {
next if ($refcall eq $call[$i]);
# for the end position, "$pos+length($call[0])-1" is already not used.
print $chr, "\t", $pos, "\t", $pos+length($refcall)-1, "\t", $refcall, "\t", $call[$i], "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
$i > 0 and $countallvar++;
}
}
} elsif ($attribute =~ m#allele\-call=([\w\/]+)#) {
@call = split (/\//, $1);
if (@call == 1) { #a simple deletion
print $chr, "\t", $pos, "\t", $end, "\t", $call[0], "\t", '-', "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
} elsif ($call[0] eq '') { #a simple insertion (single or multiple allele)
for my $i (1 .. @call-1) {
print $chr, "\t", $pos, "\t", $pos, "\t", '-', "\t", $call[$i], "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
$i > 1 and $countallvar++;
}
} else { #an indel that may have several alleles, or may require a block substitution representation
for my $i (1 .. @call-1) {
print $chr, "\t", $pos, "\t", $pos+length($call[0])-1, "\t", $call[0], "\t", $call[$i], "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
$i > 1 and $countallvar++;
}
}
} else {
$call = '0';
print $chr, "\t", $pos, "\t", $end, "\t", $call, "\t", '-', "\t", $zygosity, "\t", "$score\t$readcount\t$mutallelecount\t", join ("\t", @other), "\n";
}
} else {
die "Error: unrecognizable genotype calling program encountered (valid types are SOLiD_diBayes, AB_CNV_PIPELINE, AB_SOLiD Large Indel Tool, AB_SOLiD Small Indel Tool): <$_>\n";
}
$countvar++; #variation positions
$countallvar++; #all variants (maybe several at one variation position)
}
print STDERR "NOTICE: Finished processing $variantfile with $countline input lines\n";
print STDERR "NOTICE: Wrote variants in $countvar variation positions ($countallvar variants considering multi-allelic ones)\n";
$unknown_count and print STDERR "WARNING: $unknown_count variants with 'unknown' variation type were skipped\n";
}
sub convertSOAP {
my ($variantfile) = @_;
my ($countline, $countvar, @other);
if ($variantfile eq 'stdin') {
*VAR = *STDIN;
} elsif ($variantfile =~ m/\.gz$/) {
open (VAR, "gunzip -c $variantfile |") or die "Error: cannot read from STDIN uncompressing variant file $variantfile: $!\n";
} else {
open (VAR, $variantfile) or die "Error: cannot read from variant file $variantfile: $!\n";
}
while (<VAR>) {
s/[\r\n]+$//;
$countline++;
my @field = split (/\t/, $_);
if (@field == 18) { #snp file
my ($chr, $pos, $wt, $call, @other) = @field;
$chr =~ s/^chr//;
$includeinfo or @other = (); #unless -includeinfo is set, the other will not be printed
my $obs = $iupac{$call} or die "Error: invalid best call in <$_>\n";
my @obs = split (//, $obs);
@obs == 2 or die "Error: observed IUPAC allele $call should correspond to two nucleotide alleles: <$_>\n";
if ($obs[0] eq $wt and $obs[1] eq $wt) {
die "Error: reference alleles are identical to observed alleles: <$_>\n";
} elsif ($obs[0] eq $wt) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[1], "\t", "het\t", join ("\t", @other), "\n";
} elsif ($obs[1] eq $wt) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "het\t", join ("\t", @other), "\n";
} elsif ($obs[1] ne $obs[0]) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "het\t", join ("\t", @other), "\n";
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[1], "\t", "het\t", join ("\t", @other), "\n";
$countvar++;
} else {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "hom\t", join ("\t", @other), "\n";
}
} elsif (@field == 17) { #snp file
my ($chr, $pos, $wt, $call, @other) = @field;
$chr =~ s/^chr//;
$includeinfo or @other = (); #unless -includeinfo is set, the other will not be printed
my $obs = $iupac{$call} or die "Error: invalid best call in <$_>\n";
my @obs = split (//, $obs);
@obs == 2 or die "Error: observed IUPAC allele $call should correspond to two nucleotide alleles: <$_>\n";
if ($obs[0] eq $wt and $obs[1] eq $wt) {
die "Error: reference alleles are identical to observed alleles: <$_>\n";
} elsif ($obs[0] eq $wt) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[1], "\t", "het\t", join ("\t", @other), "\n";
} elsif ($obs[1] eq $wt) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "het\t", join ("\t", @other), "\n";
} elsif ($obs[1] ne $obs[0]) {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "het\t", join ("\t", @other), "\n";
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[1], "\t", "het\t", join ("\t", @other), "\n";
$countvar++;
} else {
print $chr, "\t", $pos, "\t", $pos, "\t", $wt, "\t", $obs[0], "\t", "hom\t", join ("\t", @other), "\n";
}
} elsif (@field == 6) { #indel file
my ($chr, $pos, $strand, $indellen, $call, $homo) = @field;
$homo eq 'Homo' and $homo = 'hom';
$homo eq 'Hete' and $homo = 'het';
$chr =~ s/^chr//;
$includeinfo or @other = (); #unless -includeinfo is set, the other will not be printed
if ($indellen =~ m/^\+(\d+)$/) { #insertion
length ($call) == $1 or die "Error: invalid record found in SOAPindel file: <$_>\n";
print join("\t", $chr, $pos, $pos, '-', $call, $homo), "\n";
} elsif ($indellen =~ m/^\-(\d+)$/) { #deletion
length ($call) == $1 or die "Error: invalid record found in SOAPindel file: <$_>\n";
print join("\t", $chr, $pos, $pos+$1-1, $call, '-', $homo), "\n";
} else {
die "Error: invalid record found in SOAPindel file: <$_>\n";
}
} else {
die "Error: invalid record found in $variantfile (18, 17 or 6 fields expected, observed ${\(scalar @field)} fields): <$_>\n";