Problems With Sam2Pindel

Question

[jason.r.gallant]

Hi all,

I'm trying to operate the PINDEL pipeline on some resequencing data that was aligned with Bowtie2. I am starting with the sam2pindel program, and things seem to proceed nicely for several hundred megabytes of output... however the program mysteriously hangs suddenly. Has anyone observed this problem before, or have any advice how better to troubleshoot the issue?

Many thanks, Jason Gallant

[Ashutosh Pandey]

Does it tell anything? Any output or any log file.

[jason.r.gallant]

Nope, no output or log, just hangs.

[PoGibas]

Have you tried bam2pindel.pl?

Answer 1

[liangkaiye]

hi Jason,

can you tell me how you run sam2pindel? did you pipe samtools view (or other ways) or use sam file as input? can you cut the bam where it went wrong and send to me [e-mail])? sam2pindel is rather simple way of selecting reads for pindel run. have you try -i and feed bowtie BAM files directly to Pindel?

I do not have bowtie bam here but would spend sometime to study bowtie sam output to optimize read selection, if this is requested by Pindel users.

Kai

[jason.r.gallant]

Hi Kai,

Thanks for your note. I am indeed piping samtoolsview into sam2pindel. I wasn't brave enough to just try feeding the bowtie2 bam files directly into pindel :)

I will try this now, and see how it goes. I will peek into the bamfile and see if I can send it to you directly.

Cheers, Jason

[liangkaiye]

great, it might be ideal to have the same data aligned with bwa and bowtie, then pass the bam files in one run to pindel. then you will see the difference clearly.

use -i option as input in the config file (assume 500 insert size): /path/to/bwa.bam 500 bwa /path/to/bowtie.bam 500 bowtie

Kai