MAF missing COSMIC, CONTEXT, and DBVS columns:
To reproduce, need to include/modify one or more scripts from OpenGenomic/pancan-maf-merge scripts (merge.py and/or mafanalysis.Rnw) and/or convingto/pancanmafmerge (annotate_vcf_cosmic.py).
Will also require CosmicCodingMuts.vcf.gz from https://cancer.sanger.ac.uk/cosmic/download?genome=37; COSMIC registration is needed to acquire this file. How important are these columns?
MAF missing COSMIC, CONTEXT, and DBVS columns:
To reproduce, need to include/modify one or more scripts from
OpenGenomic/pancan-maf-mergescripts (merge.pyand/ormafanalysis.Rnw) and/orconvingto/pancanmafmerge(annotate_vcf_cosmic.py).Will also require
CosmicCodingMuts.vcf.gzfromhttps://cancer.sanger.ac.uk/cosmic/download?genome=37; COSMIC registration is needed to acquire this file. How important are these columns?