snp identification with Haplotypecaller and SelectVariants

Question

[felipead66]

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

Answer 1

[Pierre Lindenbaum]

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.

[felipead66]

How to extract gvcf from haplotype caller?

[Pierre Lindenbaum]

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php#--emitRefConfidence