I am using Pindel (version 0.2.4w) to detect SVs for a non-model system. What I have done are:
1st. mapping the mate-pair reads to the reference genome with bwa.
2nd. I converted the sam to bam with samtools and filtered out the reads with mapping quality <20.
3rd. the duplicated reads were filtered out by Picard.
However, Pindel always crashed after several minutes and reported
"terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::at pindel.sh: line 10: 22278 Aborted "
I have tried several window sizes, from 1 to 5 million, however, I always met the same problem.
thanks
hi Kaiye,
thanks for the suggestion. I saw some people do the reverse complement for the reads of the mate pair library before the mapping step, and then do SV calling using Pindel.
I have an another question that how does Pindel handle the paired end read contamination in the mate pair libraries?