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Q: Where did my mutations go?

A: MAFs processed by MutSig may have mutations removed for one of several reasons:

  •  They are on contigs other than chr1-22/X/Y
  •  They are malformed in some way, e.g. purport to be a “mutation from C to C”, or are an unknown Variant_Classification (e.g. Targeted_Region)
  •  They are noncoding mutations or in genes absent from MutSig's list of gene definitions, or in poorly covered genes (by historic coverage metrics)
  •  They are in the “mutation blacklist,” a static list of positions observed in the past to harbor common artifacts or germline variation.
  •  They occur in patients MutSig deems to be duplicates.
Q: Where can I find a copy of the blacklist used in MutSig runs?

A: The blacklist is used to filter out recurrent mutation sites that the MutSig development team found to cause issues with the determination of significance. Because these by nature include germline mutations that may not have been part of available databases at the original generation of the MAF, we are not permitted to release it to the public.

Q: Why does your table of ingested data show that disease type XYZ has N methylation samples?

A: We ingest and support both of the major methylation platforms (Infinium HumanMethylation450 and HumanMethylation27), therefore the entries in our data table give the sum of both.  However, as noted in our June 2012 release notes, Firehose does not yet include the statistical algorithms used by TCGA AWGs to merge both of these methylation platforms into a single bolus; until those are shared we prefer meth450 over meth27 when available for a given disease type, as it gives not only greater sample counts but also higher resolution data.