To run MuTect with hg19 reference - if I use ucsc.hg19.fasta, can I use dbsnp_138.hg19.vcf and b37_cosmic_v54_120711.vcf (from the download page)? The previous forums seemed quite confusing and were not recent. Please let me know. Thank you.
@varsha You should use LiftoverVariant to lift the vcf file from b37 to ucsc. While both cosmic and dbsnp file don't affect the final variant identification.
Thank you, thats exactly what I did and it worked after adding the header
@varsha please give me some details about how to solve the problem. I found the page http://www.broadinstitute.org/gatk/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_LiftoverVariants.php