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  • problem with gsnap sam output

    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.

  • #2
    Perhaps you should try Picard's SAM validator to test whether your SAM file is valid.

    Comment


    • #3
      Thank you, I did not know of this tool and it has been very helpful.

      Comment

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