The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.