To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

how to choose from many types of dbsnp and cosmic files for MuTect input

To run MuTect, dbsnp and cosmic files need to be provided. I know there are GATK Reference bundle for hg18 and hg19 reference genome. But for my case, I use hg38 reference genome in the pre-processing steps of exome sequencing data. I plan to download dbsnp and cosmic files corresponding to the hg38 reference genome separately from NCBI and COSMIC website. But there are many types of these two files, like All.vcf, common_all.vcf, common_and_clinical.vcf, and CosmicCodingMuts.vcf, CosmicNonCodingVariants.vcf etc. I am confused about which file I need to choose as input files for MuTect.

Sign In or Register to comment.