sambamba-depth: All files must be coordinate-sorted error?
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11 months ago
MobiusT ▴ 10

I am trying to use sambamba to an indexed whole genome dataset.

basename_X $dataset
f="$(basename_X -- $dataset)"
sambamba depth base -L genomic.bed $dataset> ./reads/"$f.txt"

However, the above script gives the following error.

sambamba-depth: All files must be coordinate-sorted

What is the reason and how can I solve it?

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11 months ago

What is the reason

All files must be coordinate-sorted

how can I solve it?

samtools sort

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samtools sort $filename works in that case, right?

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samtools sort -o sorted.bam input.bam

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