cant make index file for Wheat accepted_hits.bam file

Question

[meisam.radfar]

hi i want to make index file for my accepted_hits.bam file (from tophat2) i use this:

samtools index x.bam

but i see an error that say samtools cant make x.bai index and just samtools can make x.csi index by

samtools index -c x.bam

how i can make index file x.bai (bai)

error is this:

[E::hts_idx_check_range] Region 536882696..536884035 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
[E::sam_index] Read 'A00783:167:HTLJ3DSXX:3:1427:30798:14309' with ref_name='1A', ref_length=594102056, flags=385, pos=536882697 cannot be indexed
samtools index: failed to create index for "19358.bam": Numerical result out of range

Answer 1

[ATpoint]

Some of your chromosomes are probably too long for the default bai index, see Error when trying to sort unmapped reads in samtools. so you have to use the suggested csi index.