Pindel Segmentation Fault (Version 0.2.4W)

Question

[Shaohua]

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

Answer 1

[liangkaiye]

Pindel is designed for paired-end reads. can you try new version 0.2.5 at github.com/genome/pindel

[Shaohua]

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?

Answer 2

[piyu.shettiwar]

I was running the 0.2.5 version on the paired-end reads and getting the segmentation fault. Any ideas?

Answer 3

[steve]

I encountered this exact error message a day or two ago. The issue for me was that the order of the BAM's @SQ lines (and thus the alignments, most likely) was different to the order of the chromosomes in the reference (genome) fasta file.

Rather than re-order the BAM, it was much faster for me to create a new genome fasta with nicely ordered chromosomes as defined by the BAM's header.

Some groups have decided to sort their chromosomes lexicographically and others have decided that naturally is the best sorting schema. But it doesn't matter. What matters is that the genome file you're using matches the one used to create the BAM. Order is important!

And when you're finished creating this new reference file, don't forget to index it with samtools when you're done.