I am working with a SAM file (created with hisat2) with header:
@SQ SN:chr1A LN:594006513 @SQ SN:chr1B LN:693261537 ...
When doing sorting and indexing, I get this error with samtools:
[E::hts_idx_check_range] Region 536907741..536907892 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6 [E::sam_index] Read 'read_id' with ref_name='chr1A', ref_length=594006513, flags=16, pos=536907742 cannot be indexed samtools index: failed to create index for "test.bam": Numerical result out of range
However the read falls inside the chr1A ref sequence. Any ideas why this happens? Thanks