Question: SNP + INDEL Merging Guidelines
2.6 years ago by

Say I have SNP INDEL calls for 1000 individuals. These 1000 samples were joint-called and recalibrated with GATK in 10 batches.

As a result I have 10 VCF files with SNP and INDEL calls that I would like to merge. I only have access to the VCF files, so re-calling from the BAMs is not an option.

I'm familiar with bcftools but I'm unclear on the best way forward.

  • Should I split multiallelic entries into biallelic before merging?

  • If I'm interested in rare variants, should I omit multiallelic variants?

  • Should I left align before merging? After merging? Or Both?

Thank you for any advice

merging snp indel vcf • 2.0k views
ADD COMMENTlink written 2.6 years ago by QVINTVS_FABIVS_MAXIMVS2.4k

I think your best bet would be to use GATK's merge SNPs option as I had issues merging them using vcftools/bcftools in the past. Possibly this:

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by MAPK1.7k

Yes, I believe GATK's CombineVariants is the answer.

ADD REPLYlink written 2.6 years ago by Kevin Blighe69k
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