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Should I run CombineVariants on indels and snps after VQSR/hard filtering?

Before VQSR/hard filtering, I have one single vcf file.

According to the best practice doc, I need to split it into indels and snps and run VQSR/hard filtering.

At the end, I have one filtered vcf for indels and one filtered vcf for snps.

I wanted to get one single vcf back, so I tried CombineVariants. However, I am getting two samples in the combined vcf if I run it with UNIQUIFY. I can get a vcf with only one sample using PRIORITIZE with snp over indel. Is PRIORITIZE the right way to merge?

Best Practice doc doesn't seem to mention whether to run CombineVariants after filtering. Is CombineVariants possible or desirable? If it is not desirable, does that mean downstream analysis like VariantEval should run separately for snp and indel???

Thanks a lot in advance

Answers

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