Question: Minimum base quality for Pindel
gravatar for jsneaththompson
19 days ago by
jsneaththompson0 wrote:

I've been trying to find out whether Pindel has a minimum base quality required for a base to contribute towards a variant call, but I haven't found anything by going through forums or looking at the Pindel user manual.

I have been looking at the source code on github and found this section of code in the bam2depth.cpp file:

int bam2depth(const std::string& chromosomeName, const int startPos, const int endPos, const int minBaseQuality, const int minMappingQuality, const std::vector <std::string> & listOfFiles,
          std::vector< double > & averageCoveragePerBam
   int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0;
   const bam_pileup1_t **plp;
   char *reg = 0; // specified region
   //void *bed = 0; // BED data structure
   aux_t **data;
   bam_mplp_t mplp;

I don't use C++, but it looks to me like the baseQ = 0 could be stating that Q0 is the minimum base score used by Pindel; would anyone be able to offer their own opinions on this issue?

ADD COMMENTlink written 19 days ago by jsneaththompson0
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