![]() Otherwise, it will try to determine zygosity from variant allele fractions, assuming that arguments -tum-vad-col and -tum-depth-col are set correctly to the names of columns containing those read counts. ![]() Addition of Tumor_Seq_Allele1 will be used to determine zygosity. See data/minimalist_test_maf.tsv for a sampler. Though the most useful feature is the extensive support in parsing a wide range of crappy MAF-like or VCF-like formats we've seen out in the wild. The vcf2maf and maf2maf scripts leave most of that responsibility to Ensembl's VEP, but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. And that's what this project attempts to standardize. This selection of a single effect per variant, is often subjective. But even within a single isoform, a Missense_Mutation close enough to a Splice_Site, can be labeled as either in MAF format, but not as both. To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect.
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