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how to correct this Error while building index from .bam file?

Hello all,

I encountered an error while trying to make index for a bam file. How do I correct it? by the way, my bam was generated from sam after mapping with bowtied2. Thanks

samtools index file.bam

[E::hts_idx_push] NO_COOR reads not in a single block at the end 38 -1
samtools index: failed to create index for "file.bam"
bam samtools
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updated by Ram Ram • written by jaqx008 jaqx008

validate your bam file.

what is the output of samtools view -c file.bam ?

if there is an error, it doesn't come from index but from your upstream workflow.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for your response, the problem was I did not sort the bam. I sorted it now and I dont get the error anymore. Thank you

• 1 views • link
written by jaqx008 jaqx008

1 answer

Did you sort the bam file? What was the command used to create the bam file?

• 1 views • link
written by h.mon h.mon

Oh. I did not sort it. I am sorting it now so I can make index off the sorted file. I think that should work.

• 1 views • link
written by jaqx008 jaqx008

Are you using a very old version of samtools? I'd expect a more explicit error message.

• 1 views • link
written by WouterDeCoster WouterDeCoster

Thank you, this was my mistake, Its good now. again thanks

• 1 views • link
written by jaqx008 jaqx008

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