Question: Error while generating index files using samtools
gravatar for bisht20diksha
2.0 years ago by
bisht20diksha20 wrote:

Hello. I am trying to identify differential alternative splicing between samples using splAdder. It requires sorted bam files and index files. I have sorted bam files individually using samtools script

samtools sort test.bam test_sorted

Now, I am trying to generate index file using script:

samtools index test_sorted.bam test_sorted.bai

But everytime following error appears:

[E::hts_idx_push] Region 536884677..536885767 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
samtools index: failed to create index for "cd_cnt_rt_rep1Aligned.sorted": Numerical result out of range

How to fix it?

spladder samtools • 1.6k views
ADD COMMENTlink modified 2.0 years ago by Arup Ghosh2.1k • written 2.0 years ago by bisht20diksha20
gravatar for Devon Ryan
2.0 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:
samtools index -c test_sorted.bam
ADD COMMENTlink written 2.0 years ago by Devon Ryan94k
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