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.
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.