Chadi Saad

Please found the 2 SAM files corresponding to the 2 bugs: - bug1.sam : for positions shift bug (due to InDels I think) - bug2.sam : for bug due to...

thanks for fast reply. But I have another bug now, it says [E::sam_parse1] CIGAR and query sequence are of different length [W::sam_read1] parse error at line 319 [main_samview] truncated file....

Please find it in attachement. [bug.sam.zip](https://github.com/lindenb/jvarkit/files/1138258/bug.sam.zip)

any answer please ? @sfchen

My idea is to load automatically the BAM file corresponding to the VCF file. Without having to click manually on 'load track' and search the file on the file system....

I have the same issue described above