CosmicCodingMuts.vcf.gz for hg38?

Question

[Tania]

Hi all

I downloaded CosmicCodingMuts.vcf.gz from Cosmic site. Then I use for my RNAseq somatic calling Homo_sapiens_assembly38.dbsnp138.vcf from GATK resource bundle. And also use reference: Homo_sapiens_assembly38.fasta

Where I can find Cosmic files with chr contigs for hg38?

cosmic.vcf and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information. Error details: No overlapping contigs found.
    ##### ERROR  cosmic.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT]
    ##### ERROR   reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2_KI270715v1_random, chr2_KI270716v1_random, chr3_GL000221v1_random, chr4_GL000008v2_random, chr5_GL000208v1_random, chr9_KI270717v1_random, chr9_K

Thanks

[erwan.scaon]

See also : COSMIC vcf file compatibility for Mutect2

[Tania]

Thanks erwan.scaon :)

Answer 1

[dariober]

This is the script I used to prepare the cosmic file for mutect2 (GATK 3.8). Check if it suites you (and does the right thing!). I think I had to get a user account for Cosmic first:

## Edit to put your email address:
sftp <your.name>@<foo.bar>@sftp-cancer.sanger.ac.uk

sftp> get /files/grch38/cosmic/v82/VCF/CosmicCodingMuts.vcf.gz
sftp> get /files/grch38/cosmic/v82/VCF/CosmicNonCodingVariants.vcf.gz

Convert chromosome names for GATK and combine VCFs:

zcat CosmicCodingMuts.vcf.gz | awk '{if($1 ~ "^#"){print $0} else {print "chr" $0}}' | sed 's/^chrMT/chrM/' | bgzip > CosmicCodingMuts.vcf.gatk.gz
zcat CosmicNonCodingVariants.vcf.gz | awk '{if($1 ~ "^#"){print $0} else {print "chr" $0}}' | sed 's/^chrMT/chrM/' | bgzip > CosmicNonCodingVariants.vcf.gatk.gz
tabix CosmicCodingMuts.vcf.gatk.gz
tabix CosmicNonCodingVariants.vcf.gatk.gz

bcftools concat --allow-overlaps --output-type z CosmicCodingMuts.vcf.gatk.gz CosmicNonCodingVariants.vcf.gatk.gz > CosmicMuts.gatk.vcf.gz
tabix CosmicMuts.gatk.vcf.gz
rm CosmicCodingMuts.vcf.gatk.gz* CosmicNonCodingVariants.vcf.gatk.gz*
rm CosmicCodingMuts.vcf.gz* CosmicNonCodingVariants.vcf.gz*

[Tania]

Thanks dariober, I already downloaded the file, converting the chr 1 thing is what I wanted, will try the code now. Very much appreciated.