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 :
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 ?