I'm trying to run bam-readcount on a MacOS X 10.9.5 machine.
I'm aware that bam-readcount returns a segfault when asked to process an entire bam file, that's why I order it to run one chromosome at a time.
Here's a example command I tried:
bam-readcount -f 7Dref_all.fa 7dmerge_dedup.bam XV > 7dmerge_dedup_chrXV.readcount
I get the following warnings, along with an empty output file:
Minimum mapping quality is set to 0
Expect library: 7d in BAM
Segmentation fault: 11
Anything wrong with my syntax ? I played with it a bit, to no avail. Tried several different bam files, all of them are fine in other applications, as far as I can tell. They were generated by picard.
Thanks a million