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Merge pull request #92 from broadinstitute/nh_update_genotype_concord…
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…ance_scheme

updating the genotype concordance scheme to have called variants that
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@nh13
nh13 committed Oct 16, 2014
2 parents f12398c + a837a28 commit 879fc02
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Showing 5 changed files with 10 additions and 10 deletions.
8 changes: 4 additions & 4 deletions src/java/picard/vcf/GenotypeConcordanceScheme.java
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Expand Up @@ -85,10 +85,10 @@ public GenotypeConcordanceScheme() {
addRow(CallState.HOM_VAR2, NA, NA, FP_FN, TP_FN, FP_FN, NA, NA, NA, NA, NA, NA);
addRow(CallState.HOM_VAR3, NA, NA, NA, FP_FN, NA, NA, NA, NA, NA, NA, NA);
addRow(CallState.NO_CALL, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.VC_FILTERED, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.GT_FILTERED, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.LOW_GQ, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.LOW_DP, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.VC_FILTERED, EMPTY, TN_ONLY, TN_FN, FN_ONLY, FN_ONLY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.GT_FILTERED, EMPTY, TN_ONLY, TN_FN, FN_ONLY, FN_ONLY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.LOW_GQ, EMPTY, TN_ONLY, TN_FN, FN_ONLY, FN_ONLY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.LOW_DP, EMPTY, TN_ONLY, TN_FN, FN_ONLY, FN_ONLY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);
addRow(CallState.IS_MIXED, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY, EMPTY);

validateScheme();
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2 changes: 1 addition & 1 deletion .../CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_detail_metrics
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@@ -1,7 +1,7 @@
## htsjdk.samtools.metrics.StringHeader
# picard.vcf.GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 MIN_DP=40 INTERSECT_INTERVALS=true MIN_GQ=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Oct 07 16:12:54 EDT 2014
# Started on: Thu Oct 16 16:18:19 EDT 2014

## METRICS CLASS picard.vcf.GenotypeConcordanceDetailMetrics
VARIANT_TYPE TRUTH_SAMPLE CALL_SAMPLE TRUTH_STATE CALL_STATE COUNT
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4 changes: 2 additions & 2 deletions ...CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_summary_metrics
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@@ -1,11 +1,11 @@
## htsjdk.samtools.metrics.StringHeader
# picard.vcf.GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 MIN_DP=40 INTERSECT_INTERVALS=true MIN_GQ=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Oct 07 16:12:54 EDT 2014
# Started on: Thu Oct 16 16:18:19 EDT 2014

## METRICS CLASS picard.vcf.GenotypeConcordanceSummaryMetrics
VARIANT_TYPE TRUTH_SAMPLE CALL_SAMPLE HET_SENSITIVITY HET_PPV HOMVAR_SENSITIVITY HOMVAR_PPV VAR_SENSITIVITY VAR_PPV
SNP NA12878 NA12891 0.728261 0.703297 0.77027 0.75 0.746988 0.725146
SNP NA12878 NA12891 0.67 0.703297 0.76 0.75 0.708571 0.725146
INDEL NA12878 NA12891 ? ? ? ? ? ?


2 changes: 1 addition & 1 deletion .../CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_detail_metrics
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@@ -1,7 +1,7 @@
## htsjdk.samtools.metrics.StringHeader
# picard.vcf.GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 MIN_GQ=40 INTERSECT_INTERVALS=true MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Oct 07 16:12:46 EDT 2014
# Started on: Thu Oct 16 16:14:31 EDT 2014

## METRICS CLASS picard.vcf.GenotypeConcordanceDetailMetrics
VARIANT_TYPE TRUTH_SAMPLE CALL_SAMPLE TRUTH_STATE CALL_STATE COUNT
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4 changes: 2 additions & 2 deletions ...CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_summary_metrics
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@@ -1,11 +1,11 @@
## htsjdk.samtools.metrics.StringHeader
# picard.vcf.GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 MIN_GQ=40 INTERSECT_INTERVALS=true MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Oct 07 16:12:46 EDT 2014
# Started on: Thu Oct 16 16:14:31 EDT 2014

## METRICS CLASS picard.vcf.GenotypeConcordanceSummaryMetrics
VARIANT_TYPE TRUTH_SAMPLE CALL_SAMPLE HET_SENSITIVITY HET_PPV HOMVAR_SENSITIVITY HOMVAR_PPV VAR_SENSITIVITY VAR_PPV
SNP NA12878 NA12891 0.708738 0.690722 0.77027 0.732558 0.734463 0.710383
SNP NA12878 NA12891 0.701923 0.690722 0.76 0.732558 0.726257 0.710383
INDEL NA12878 NA12891 ? ? ? ? ? ?


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