HG19 Cosmic VCF

Question

[M. Khan]

I've been trying to find a cosmic vcf file that I would be able to use with hg19 as the reference in MuTect but I can't seem to find it. I downloaded the Cosmic coding mutants VCF file v68 but it's still giving me the error:

Input files /Users/iMac/Downloads/CosmicCodingMuts_v68.vcf and reference have incompatible contigs: No overlapping contigs found.

I read that I need to use LiftOverVariants to create this vcf file but I don't know how to do that. Thank you for your help.

[Sam]

Maybe check if both the vcf and your reference uses the same chromosome representation? e.g. whether if they both have the chr in front. Usually, this is the most common reason for that error to appear

[M. Khan]

I got LiftoverVariants to work, do you happen to know what it means to add a line to the header of the code? I don't know how to follow this:

I had to add the following line to the header, and then it was successful:

##INFO=<id=somatic,number=0,type=flag,description="somatic event"="">

Answer 1

[Sean Davis]

The most recent COSMIC VCF files are here.

You will need to create a login to access them. They are relative to GRCh37 which is the same as hg19. The one difference is that the chromosome names (at least for the autosomes and sex chromosomes) will not contain "chr" before them as @Sam notes in a comment. After you make sure that your files either all have or do not have the "chr" prefix before the chromosome number, things should be fine. There is no need to perform a liftover.

[M. Khan]

Thank you for help! How do I add "chr" before the chromosome names in the cosmic file?