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Combine SNPs and INDELs when using Haplotype Caller
Just wondering what is the best way to combine SNPs and INDELs after using Haplotype caller to get a single VCF. It seems straight forward with UnifiedGenotyper, since there is eparate VCF for each, and they are recalibrated separately. But the Haplotype caller, they are relibrated indivisually in the already combined file.
I have recalibrated SNPs and INDELs separately, but not sure how to combine them. since both recalibrated VCFs contain allvariants, not sure combineVariants can handle it.