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how do you find the sequence of a long insertion? #441

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jshenVaxart opened this issue Nov 2, 2023 · 1 comment
Open

how do you find the sequence of a long insertion? #441

jshenVaxart opened this issue Nov 2, 2023 · 1 comment

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@jshenVaxart
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I get this output in my vcf file
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
Ad-ED119.9_ECJ9+CMV-JnJ-StabWuS-SV40-dsRNA 18587 Sniffles2.INS.3S0 N 56 PASS PRECISE;SVTYPE=INS;SVLEN=8050;END=18587;SUPPORT=1609;COVERAGE=87914,88129,88187,88034,87662;STRAND=+;NM=0.032;AF=0.099;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=1608 GT:GQ:DR:DV ./.:60:79428:8759

so the insertion is at position 18587, but I can't figure out what the sequence is. Is there a way to print that out?

Thanks

@jshenVaxart
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As an update, I have tried --genotype-vcf and it did not print out the genotype ie:

sniffles
--input /output/barcode01/barcode01_ngmlr_sorted.bam
--ref /output/reference/reference.fa
--genotype-vcf /output/barcode01/barcode01_ngmlr.vcf
--non-germline
--vcf /output//barcode01/barcode01_ngmlr_altPrinted.vcf

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