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What does one do with the raw VCF output of joint genotyping many gVCF files?
I have been following the best practices outline for calling SNPs on our samples, but I'm a little confused as to what to do with the VCF file produced following the joint genotyping/genotypeGVCFs step.
I understand the principle of gVCF calling for the most part, but my confusion is what are we to do with the VCF file once we do the joint genotyping step? We are looking at a F1 mapping population of a non-model organism, so does this VCF file have individual progeny (bam file names) indicated within it? I think not since I can't find any of the sample names while scrolling through it.
Can this VCF file be used to construct a pedigree file to use during genotype refinement? Should it be somehow fed back into Haplotypecaller to inform on likely calls during a second round of variant calling? Do you use it to go back to the individual gVCF files to extract the high confidence variants?
There seems to be a good amount of literature on the Broad websites about what a gVCF file is and how to perform joint genotyping, but not much direction about what to do with the joint genotyped VCF file once it is produced.
Any advice or referral to other walkthroughs/guides would be very appreciated.
[extra project information: My project involves calling SNPs across a mapping population for a non-model organism with the intent of mapping a trait. The goal is to produce robust SNP calls for each individual progeny (of which we have 30 currently, and >60 in the near future) and the two parents. We only have halfway-decent sequencing coverage of ~10-20x for each sample, which is thus why doing gVCF calling and joint genotyping sounds attractive to us. Since we work on a non-model, we also lack previously produced "gold standard" SNP sets or other resources allowing us to refine genotypes.]