Question: Minimum base quality for Pindel
gravatar for jsneaththompson
12 months ago by
jsneaththompson50 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 12 months ago by jsneaththompson50
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1439 users visited in the last hour