Entering edit mode
6.6 years ago
jsneaththompson
▴
100
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?