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snp identification with Haplotypecaller and SelectVariants

I want to find the snps for 10 cultivars of almond. Which of the following is correct:

1. Use haplotypecaller to find snps for each cultivar (based on the reference genome), then use selectvariants to find true snps and finally filter the snps with variant filter

or

2.Use haplotypecaller to find snps using as input the bam files for ALL cultivars, then use selectvariants to find true snps and finally filter the snps with variant filter

snp gatk
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by felipead66 felipead66

1 answer

solution 2 is easier because you'll get all the samples for a given variant. It's easier to filter. If your number of samples is too high you can use g.vcf files: https://gatkforums.broadinstitute.org/gatk/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf

whith solution 1, after merging, you don't know if a missing genotype was HOM_REF or NO_CALL.

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written by Pierre Lindenbaum Pierre Lindenbaum

How to extract gvcf from haplotype caller?

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written by felipead66 felipead66

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