Entering edit mode
7.0 years ago
ari.nazarian
▴
10
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?
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