Haplotype Calling Using GATK HaplotypeCaller to Get Exact 35718025 Positions/Loci
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5 months ago
yenon118 • 0

Hi,

I have a VCF file that has 35718025 positions/loci. I am trying to add more accessions (let's say accession1, accession2, and accession3) into this VCF using bcftools merge. When I perform haplotype calling using the GATK HaplotypeCaller, how can I output exact 35718025 positions/loci for the accession1, accession2, and accession3?

I have tried using GATK HaplotypeCaller --force-call-filtered-alleles --alleles <the VCF file that has 35718025 loci>, but the output VCF files have more than 35718025 positions/loci. Does anybody have any suggestions for me to solve this problem?

GATK HaplotypeCaller HaplotypeCalling • 320 views
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what is an "accession" ?

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Accession and sample are the same things. The Bcftools use the word sample in their manual. You can use bcftools query -l <VCF file> to print out all the accessions/samples in your VCF file.

https://en.wikipedia.org/wiki/Accession_number_(bioinformatics)

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