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.
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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