Whitelist for homozygous deletions

[lima1]

The current cutoff for homozygous deletions is large because we rarely see such huge deletions at MTAP/CDKN2A. Might be better to decrease the default and add a whitelist of known deletions.

• [ ] Query TCGA for most common deletions.

• [ ] Provide whitelist for hg19/hg38

• [ ] Use size distribution of whitelist for finding good size cutoffs, understand how SNP6 cutoffs translate to small targets with 150-200kb off-target bins.

• [ ] Do not count known deletions to max.homozygous.loss cutoffs.