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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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translocations only reported between 2 chromosomes #7

Open joelmartin opened 9 years ago

joelmartin commented 9 years ago

on my rice samples, translocations are only being reported between Chr1 and Chr10, in the stdout I see near equal numbers of lines like adding interchr Chr2 25750649 25751533 884 Chr3 23349705 23350589 involving all chromosomes so i'm sure it's not a true result, the available reference is a different strain and translocations are expected.

I can make example data available but I don't have a good idea on how to cut the size down for translocations. a bam file is ~15gb

liangkaiye commented 9 years ago

you could check RP file, which is the read-pair result summary. The INT file gives you split-read alignment if there is a hit. You could cut the local regions of both chromosomes involved in.

Kai

On 12/22/14, 7:48 PM, Joel Martin wrote:

on my rice samples, translocations are only being reported between Chr1 and Chr10, in the stdout I see near equal numbers of lines like adding interchr Chr2 25750649 25751533 884 Chr3 23349705 23350589 involving all chromosomes so i'm sure it's not a true result, the available reference is a different strain and translocations are expected.

I can make example data available but I don't have a good idea on how to cut the size down for translocations. a bam file is ~15gb

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/7.

joelmartin commented 9 years ago

Unfortunately that's giving me correct results. I've tried with up to four regions containing translocations of Chr1 <-> Chr2 and Chr1 <-> Chr10.