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Old 11-03-2010, 02:20 AM   #1
lindseyjane
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Location: Oxford

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Default 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.
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Old 11-03-2010, 08:13 PM   #2
zee
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Perhaps you should try Picard's SAM validator to test whether your SAM file is valid.
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Old 11-04-2010, 04:27 AM   #3
lindseyjane
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Thank you, I did not know of this tool and it has been very helpful.
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