PindelRecordParser - investigate accurate VAF

[keiranmraine]

Currently we just parse out the reads that Pindel calls, it would be nice to evaluate that an event has no normal support and then run ssearch36 over reads in the primary BAM to generate an accurate VAF upfront and then use new values for the flagging/filtering.

[liangkaiye]

The new pindel reports the numbers of reads supporting normal and tumor allele. But as we cannot split reads near edges, the VAF is always underestimated. There is one competitive mapping perl script in ICGC validation evaluation exercise but it is slow as it extracts reads and calls bwa for mapping.

Sent from my iPhone

On Dec 11, 2015, at 11:59, Keiran Raine notifications@github.com wrote:

Currently we just parse out the reads that Pindel calls, it would be nice to evaluate that an event has no normal support and then run ssearch36 over reads in the primary BAM to generate an accurate VAF upfront and then use new values for the flagging/filtering.

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