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?