Question: samtools mpileup with -l option
gravatar for qmemcm
3.4 years ago by
United States
qmemcm30 wrote:


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!

snp sequence • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Petr Ponomarenko2.6k • written 3.4 years ago by qmemcm30
gravatar for Petr Ponomarenko
3.4 years ago by
United States / Los Angeles /
Petr Ponomarenko2.6k wrote:

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 for the developers. Thank you, Petr

ADD COMMENTlink written 3.4 years ago by Petr Ponomarenko2.6k
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