Could someone pleases suggest hot to interpret and bypass the following Pindel error:
pindel: reader.cpp:427: bool ReadInBamReads_RP_Discovery(const char, const string&, const string, std::vector<rp_read>&, std::vector<rp_read>&, int, std::string, const SearchWindow&): Assertion `idx' failed. Initializing parameters...
I'm running Pindel on a 25 small indexed bam files for PDGFRA e12 (Ion Torrent) using chr4 reference.
- I build a list of all the files and insert size
- I run pindel: $pindel -f $fastafile -i $configfile -c ALL -o $outputfolder";
- I run pindeltovcf: $pindeltovcf -p $deloutput -r $fastafile -R hg19-GRCh37 -d 200903 -v $delvcf"
For the most part it is working very well. The problem is that Pindel crashes when it encounters a bad bam file. Is there a setting that will allow Pindel to continue analyzing other good file and not to crash?
Although this is not an answer, you should try validating your bam/sam files with picard tools ( http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile) before your run pindel on it. Unless it is a bug in pindel, a bad bam is not good for downstream analysis. They are supposed to be fixed, IMHO.
by bad I mean if a particular sample failed and bam has no reads.