Question: Merging VCFs: Illumina/GATK and LoFreq
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gravatar for ari.nazarian
2.4 years ago by
ari.nazarian10
ari.nazarian10 wrote:

I have VCFs from a number of different tumor samples sourced mostly from two different variant callers that I'm trying to merge onto one sheet: GATK (via an Illumina MiSeq machine) and LoFreq. The end goal is to upload the merged VCF to CRAVAT for easier visualization/interpretation of variant information.

I'm struggling to figure out how to merge variants, though---neither vcf-merge nor CombineVariants have been able to do this successfully.

Does anyone have any experience with merging these VCFs generated by these specific variant callers?

miseq vcf variant calling • 1.1k views
ADD COMMENTlink written 2.4 years ago by ari.nazarian10

I'm struggling to figure out how to merge variants, though---neither vcf-merge nor CombineVariants have been able to do this successfully.

so, what is the problem here.

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum122k

I've just run into so many different errors that I was hoping I didn't have to go into the weeds but here's a brief overview of the initial issue I'm having (not even considering the errors when I try to manipulate the vcfs, like adding columns with sed and so forth:

I ran vcf-merge on two vcfs, one generated from GATK: GATK VCF ...another from LoFreq: LOFREQ VCF ...and this was the output merge.vcf: BADMERGE VCF ...and the corresponding output in Terminal: MERGE OUTPUT I want them to look more like this: GOOD MERGE

I've tried adding an extra column and Sample ID field to the LoFreq one but to no avail. I'm looking for pointers on how I can add columns and a sample ID to LoFreq vcfs to successfully merge this with GATK vcfs.

ADD REPLYlink written 2.4 years ago by ari.nazarian10

It's clearly not the same 'dictionary'; one set of VCF have a 'chr' prefix in the chromosome names, the other not. They should all have the very same names than defined in the REFerence file

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Pierre Lindenbaum122k
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