Apologies if this was addressed elsewhere, but I have looked carefully through the documentation. Simply put: using the joint analysis pipeline of GATK's HaplotypeCaller (-ERC GVCF) -> CombineGVCFs-> GenotypeGVCFs, are SNPs called when they are fixed in only 1 sample? For example, imagine 3 samples total, where the correct genotypes should be: A/A, A/A, T/T. Will this variant be called correctly, given sufficient coverage/quality? This is very important to what I am trying to accomplish, as I only have 3 samples, and would like to analyze SNPs that are fixed between samples. It's unclear to me that this pipeline will work, since HaplotypeCaller will not see any find these variants within samples individually. But maybe GenotypeGVCFs finds them? This is not clearly documented.
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