gravatar for meisam.radfar

2 hours ago by

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

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