Question: Combine several VCF files
gravatar for Max Ivon
17 months ago by
Max Ivon120
Russian Federation
Max Ivon120 wrote:

I've performed variant calling with two callers. One calls haplotypes and other calls mutations as single variants. As a result I have two VCF files where sometimes identical variants are written in different forms. For example: One file:

chr1    61987   .       AAG     GAC

Another file:

chr1    61987   .       A       G
chr1    61989   .       G       C

Obviously, mutations in the second file are from single haplotype and in the final VCF file i need only single record as in the first file. I've tried to use bcftools merge to combine VCF files, but I get the following:

chr1    61987   .       AAG     GAC,GAG

Which will lead to wrong annotation. So is there any software to combine these two VCF files into single one, so all single variants would disappear?

bcftools vcf • 387 views
ADD COMMENTlink modified 17 months ago by Brice Sarver3.6k • written 17 months ago by Max Ivon120
gravatar for Brice Sarver
17 months ago by
Brice Sarver3.6k
United States
Brice Sarver3.6k wrote:

A solution with the GATK (pre-4.0): LeftAlignAndTrimVariants. You can split or combine multiallelic records with bcftools norm.

ADD COMMENTlink written 17 months ago by Brice Sarver3.6k

I'd actually recommend vt-norm/vt-decompose over bcftools norm, because vt leaves a trail so the changes it makes are trackable (it preserves old variant info [chr:pos:ref:alt] in an INFO attribute).

ADD REPLYlink modified 17 months ago • written 17 months ago by Ram32k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1636 users visited in the last hour