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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Revamping the --somatic_p code in pindel2vcf.cpp #69

Open JohnMCMa opened 7 years ago

JohnMCMa commented 7 years ago

This fixes several bugs involved in the --somatic_p flag in pindel2vcf.

  1. BUGFIX: The somatic p-value is written to the INFO string without a tag. A tag SPV (from the VarScan equivalant) is added to hold this data.
  2. BUGFIX: pindel outputs prior to 0.2.4u don't have ref support count, which may lead to unpredictable results. As a result, the p-values will not be written and a warning will be given to the user if this flag is turned on and the file is of the old format.
  3. BUGFIX: The Fisher's test algorithm implemented used in kfunc.c is copied verbatim to this file but never used. It is now implemented instead of a factorial-based method which is unstable and gives out too much NaN.

This should fix #51 .