Hello,
I am using samtools v 1.2 on a machine with Ubuntu 14.04.2 and I am trying
to generate a SNP table from sorted bam files (generated from a GBS library
prep) aligned to a reference. So far I have used bwa for the alignment,
samtools view to convert sam to bam, samtools sort, and samtools index.
Those are all working fine, but when I use samtools mpileup, I get a
segmentation fault. I think it is because I am trying to pass mpileup a
list of positions to include from the reference with the -l flag (I don't
get a seg fault if I leave out the list of positions):
samtools mpileup -g -b ~/Data/alignments/bamfilenames.txt -f
/Data/alignments/reference.fa -l ~/Data/alignments/positions_to_include.txt
> fish_snps.bcf
This returns "segmentation fault (core dumped)." It also segaults if I just
pass it a single bam file, rather than a list of bam files. How does the
list of positions file need to be formatted? Is this what could be causing
the segfault?
Thanks for any help,
Sierra
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