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genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Erreur de segmentation (core dumped) #71

Open sheitandard opened 7 years ago

sheitandard commented 7 years ago

Hi,

I am using Pindel version 0.2.5b9, 20160729 and I got a segmentation fault. I have a genome with 2 chromosomes and it works fine with the first but when starting the 2nd, it throws an error right away: pindel-f bEYY1013_combined.fa -i BC72_pindel.txt -o output_bEYY1013/bEYY1013

[...] Looking at chromosome chr2 bases 1 to 1072315 of the bed region: chromosome chr2:1-1072315 Erreur de segmentation (core dumped)

I tried to take a smaller window down to 0.5 but same problem. I tried also -l false -k false but same problem. My BC72_pindel.txt is just this (with tab separation): BC72_bEYY1013_sorted.bam 300 BC72_DEL

have you ever seen this before?

EWLameijer commented 7 years ago

Such segmentation faults usually mean that the computer gets out of memory. It mostly happens when there are strongly repetitive regions, like telomers or centromeric regions (or mitochondria), where coverage can be extremely high. I suspect that may be the case for you, you may want to try pindel with the -j or -J options, eliminating regions with suspiciously high coverage.