In order to convert a bioinformatic file from CRAM to BAM format, I naively used the samtools command available on a cluster but got this error:
samtools view -T reference.fa -b -o output.bam input.cram [sam_header_read2] 3366 sequences loaded. [sam_read1] reference 'VN:1.4' is recognized as '*'. Parse error at line 1: invalid CIGAR character |
After a few commands trying to fix the issue, I realised that the error message contained the SAM label. This indicates that samtools version is a bit old. And indeed it was. I then used version 1.6 of samtools and it worked out of the box.
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