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(MuTect2) Combining 2 COSMIC vcf

I just got a hold of CosmicCodingMuts.vcf and CosmicNonCodingVariants.vcf which I would like to use for Mutect2. These were built from grch37 assembly and it seems that I need to have these resorted against my reference genome (ucsc.hg19.fasta.dict).

I found a previous post concerning this issue and used the following command

grep "^#" CosmicCodingMuts_v64_02042013_noLimit.vcf > VCF_Header
grep -v "^#" CosmicCodingMuts_v64_02042013_noLimit.vcf > Coding.clean
grep -v "^#" CosmicNonCodingVariants_v64_02042013_noLimit.vcf > NonCoding.clean
cat Coding.clean NonCoding.clean | sort -gk 2,2 | awk '{print "chr"$0}' | perl sortByRef.pl --k 1 - ucsc.hg19.fasta.fai > Cosmic.hg19
cat VCF_Header Cosmic.hg19 > Cosmic.hg19.vcf

But I end up with an empty vcf with just the header. Any input will be greatly appreciated. Thank you.

Best Answer


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