Hi,

After the execution of tophat-fusion. I want to visualize the alignment in IGV. So with the sam output file I execute samtools to convert it in a bam file :

So :

samtools view -bS -o M267T0fusion.bam accepted_hits.sam

It gives me this error :

[samopen] SAM header is present: 28 sequences.
[sam_read1] reference 'HSA4-HSA20' is recognized as '*'.
Parse error at line 133: invalid CIGAR operation
[bam_header_read] EOF marker is absent. The input is probably truncated.

Anyone has an idea on how resolve this error ?

Thanks,

N.