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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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Bug in samtools 0.1.18, request update to newer version #9

Open archaephyrryx opened 9 years ago

archaephyrryx commented 9 years ago

Samtools version 0.1.18 has a number of bugs that cause pindel to segfault under certain conditions (e.g. using a different reference genome than the one used to align the bam file) with no descriptive error messages or clear diagnostic information. Samtools 0.1.18 is out of date and is no longer maintained. Can pindel transition to work with newer versions of samtools that have been debugged and/or are actively maintained?

liangkaiye commented 9 years ago

sounds like a good suggestion. we will upgrade Pindel along with samtools.

please give us sometime.

On 3/25/15 9:09 PM, Peter Duchovni wrote:

Samtools version 0.1.18 has a number of bugs that cause pindel to segfault under certain conditions (e.g. using a different reference genome than the one used to align the bam file) with no descriptive error messages or clear diagnostic information. Samtools 0.1.18 is out of date and is no longer maintained. Can pindel transition to work with newer versions of samtools that have been debugged and/or are actively maintained?

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/9.