problem with gsnap sam output

[lindseyjane]

I have used the gsnap tool to align short reads against a reference and obtained sam output using the flag -A sam.
The sam file looks ok but when I try to convert it to a bam file then I get a segmentation fault:

samtools view -bS -t /path/to/referencefolder/gmapdb/reference.fasta.fai -o test.bam tissue.ref.sam
Segmentation fault

Any ideas how I can solve this please?Thanks.

[zee]

Perhaps you should try Picard's SAM validator to test whether your SAM file is valid.

[lindseyjane]

Thank you, I did not know of this tool and it has been very helpful.