Hello, I aligned fastq files with bwa and tried to convert sam file to bam file, and got the following error:
[samopen] SAM header is present: 24 sequences.
[sam_read1] reference 'XT:A:U' is recognized as '*'.
Parse error at line 187684275: invalid CIGAR character
Aborted
When I check the line:187684275, it's like this:
HS2000-612_106:3:1202:15375:79174 13 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100
Apparently in the 3rd column where the chrmosome should appear there is XT:A:U. Does anyone know how to avoid this? Or how to do the sam2bam convertion successfully in such case?
Thank you!
[samopen] SAM header is present: 24 sequences.
[sam_read1] reference 'XT:A:U' is recognized as '*'.
Parse error at line 187684275: invalid CIGAR character
Aborted
When I check the line:187684275, it's like this:
HS2000-612_106:3:1202:15375:79174 13 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100
Apparently in the 3rd column where the chrmosome should appear there is XT:A:U. Does anyone know how to avoid this? Or how to do the sam2bam convertion successfully in such case?
Thank you!
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