SNP + INDEL Merging Guidelines
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
• 4,246 views
•
link
written
by
QVINTVS_FABIVS_MAXIMVS
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Multiallelic variants when merging VCF's with GLnexus
written by Michal Frenkel •
-
Split plink files from multiallelic to biallelic
written by MAPK
-
Removing both duplicates from a VCF
written by john.michel.rouhana •
-
Criteria for merging multiple VCF files
written by seta
-
Principal component analysis for microbial SNP
written by Bioblazer
-
Calculating Fst for Multiallelic variants in VCFs
written by ma17 •
-
When should you left-align INDELs (and why?)
written by QVINTVS_FABIVS_MAXIMVS
-
What's 1000 Genome indel calls??
written by 2012secondseason •
-
Multiple regression for indel data in plink
written by doommonk •
-
1000Genome Project To Cover Gc-Rich Region?
written by michealsmith
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
Yes, I believe GATK's CombineVariants is the answer.