I am currently trying to perform germline variant calling for human, however, I am somewhat stuck at the VQSR step. A big problem is, that all the links ("method documentation", "parameter recommendations" and "tutorial") for the current version of the VaraintRecalibrator are dead, i.e. just lead to the homepage. Thus, I dont really know what to do, and what options I should use, e.g. for the prior (I barley find any documentation what exactly that is, or what a good default value is).
Furthermore, I am having difficulties, because I am using the GRCh37 reference genome (hs37d5.fa) and I can only find "high confidence" SNPs for the GRCh38 reference genome in the resource bundle from the Broad.
Is it possible to simply download all 1000g variants (from here), combine and filter them for SNP and INDELs respectively, and then use them as the training set?
I would be very grateful is somebody could help me out.
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