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Is BED file generated by bametobed sorted ?
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15 months ago
pacman • 50
United States

We use bamtobed to covert bam files to bed files. I am wondering if the output is sorted by default , because our output bed files seems to be sorted by chromosome and position. I am asking this question because we are using bedtools to calculate coverage with large bam files which takes up a lot of memory. It was suggested to pre-sort the bed files before running bedtools coverage in the documentation to help reduce the memory usage. However, sorting on bash , even running parallel with 8 cores, is still time-consuming. So, it would be great if anyone can confirm bamtobed does that already .

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I don't think you need to convert BAM to BED in order to take advantage of the -sorted option of coverageBed. Just pass the bam file to -a with the -sortedand possibly the -g option enabled.

Anyway, I would guess the conversion BAM to BED doesn't change the order of records so if your BAM is sorted the BED output will be sorted as well.

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14 months ago
Seattle, WA USA

You could use bam2bed to make a sort-bed-sorted file:

$ bam2bed < reads.bam > reads.bed
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