bnoyvert

Thank you @tjiangHIT for looking into the issue. I agree with the two ways to overcome the problem, that you suggested. It would make sense indeed if cuteSV displayed an...

Hi @tjiangHIT , I found the reference fasta file that was used to create the bam file attached above: `https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz` Running cuteSV with the proper reference didn't change anything: the...

Hi @tjiangHIT , I believe I found the source of the error. In this bam file occasionally some reads have `SA:Z` tags that look like `SA:Z:1,1589483,+,*,254,0;`, where the local cigar...