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does GATK offers to match alleles in two vcf files? #8681

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RezwanCAAS opened this issue Feb 7, 2024 · 0 comments
Open

does GATK offers to match alleles in two vcf files? #8681

RezwanCAAS opened this issue Feb 7, 2024 · 0 comments

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@RezwanCAAS
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Hi GATK, I have done the steps, i.e., 1)haplotypecaller 2)combineGVCF 3) GenotypeGVCF. Now I am interested in performing the allele matching between two samples, like whether the alleles are the same or different at a particular chromosomal location. Does GATK offer to perform this test? if yes, then which function in GATK will be preferable?
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@RezwanCAAS