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samtools NO_COOR reads not in a single block at the end 6 -1

Hi,

I received this error from issuing samtools index -@ 20 reads_aln.bam (samtools v1.9). I googled it and couldn't find it. The solution was to first sort the bam file. 

samtools sort -@ 20 -O BAM reads_aln.bam > reads_aln.sorted.bam && samtools index -@ 20 reads_aln.sorted.bam

Best,

P

alignment
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updated by ATpoint ATpoint • written by Pablo González • Pablo González

Is this now a question or do you want to share your experience? It is indeed necessary to sort BAM before indexing, check the manual: https://www.htslib.org/doc/samtools-index.html

Index a coordinate-sorted BGZIP-compressed SAM, BAM or CRAM file for fast random access (...)

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written by ATpoint ATpoint

It was not a question (neither a tutorial), but posted as question with solution.

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written by Pablo González • Pablo González

Ok, thanks for sharing. Since this is common knowledge from the manual I will close it though.

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written by ATpoint ATpoint

Hello Pablo González!

We believe that this post does not fit the main topic of this site.

Not a question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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