Question: SNP + INDEL Merging Guidelines
0
gravatar for QVINTVS_FABIVS_MAXIMVS
2.6 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

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: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2172 users visited in the last hour
_