More careful whitelisting of known somatic variants

[ckandoth]

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]

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]

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