Dear samtools staff, I would like to ask help about samtools index. The thing is I failed to generate indexed.bam.bai. Here is the error msg:
$ samtools index -b -@ 20 aln.sorted.cy201704.bam [E::hts_idx_check_range] Region 536856988..536888726 cannot be stored in a bai index. Try using a csi index [E::sam_index] Read 'm64291e_211224_041609/132253067/22850_47574' with ref_name='chr1', ref_length=759857066, flags=16, pos=536856989 cannot be indexed samtools index: failed to create index for "aln.sorted.cy201704.bam": Numerical result out of range I guess there are some very long contigs/chromosomes in aln.sorted.cy201704.bam. I know I should and actually have generated the csi index in this case. But the next step in my plan is to call the variants. Those callers I know, like sniffles, SVIM, only accept BAI index as input. Do you have suggestions for this situation? Maybe there is a caller that can take CSI index as input? Or there is a way to convert CSI index to BAI index? Thank you fou your time. I'm looking forward to your reply. Regards, Ruixue PhD Candidate | Jinzhong Fu’s Lab Department of Integrative Biology University of Guelph 50 Stone Rd E | Guelph, ON | N1G 2W1
_______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
