samtools mpileup with -l option

Question

[qmemcm]

Hi!

I have a list of SNP calls and I am trying to run samtools mpileup command with the -l option on this list of calls.

The documentation states that I can specify the list file in a list format, which is a two column file with chrom and pos, respectively. When I run the command samtools mpileup -l snps.list -O sample.bam, I get the correct output for the first row of my list file, but then samtools simply hangs and I don't get any further output.

[As an aside, I am using the -O option to obtain the base positions on the reads that align to the given chrom Position in my file.]

Any thoughts on what I could be doing wrong?

Thank you!

Answer 1

[Petr Ponomarenko]

Hi qmemcm, Could you please share files you used and the version of the samtools? I was not able to replicate your situation with mockup files. It sounds like an issue with the program and you may post it on github https://github.com/samtools/samtools/issues for the developers. Thank you, Petr