Merging VCFs: Illumina/GATK and LoFreq
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?
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ari.nazarian •
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so, what is the problem here.
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:
...another from LoFreq:
...and this was the output merge.vcf:
...and the corresponding output in Terminal:
I want them to look more like this:
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.
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