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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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More careful whitelisting of known somatic variants #102

Open ckandoth opened 7 years ago

ckandoth commented 7 years ago

The current gist to download the ExAC VCF and whitelist known somatic events, will also inadvertently whitelist indels that overlap these known somatic events. Fixing this will take some work. This is a low priority now.

ckandoth commented 7 years ago

To fix this, the hotspots events need to be in VCF format, but the downside is that we miss novel ALT alleles at known hotspot loci. Tough tradeoff.

ckandoth commented 6 years ago

All the hotspots and allele changes observed in a MAF-like format here - https://github.com/mskcc/ngs-filters/blob/master/data/hotspot-list-union-v1-v2.txt