Question: Is BED file generated by bametobed sorted ?
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gravatar for pacman
2.4 years ago by
pacman70
United States
pacman70 wrote:

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 .

ADD COMMENTlink modified 2.4 years ago by Alex Reynolds31k • written 2.4 years ago by pacman70

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.

ADD REPLYlink written 2.4 years ago by dariober11k
0
gravatar for Alex Reynolds
2.4 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

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

$ bam2bed < reads.bam > reads.bed
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Alex Reynolds31k
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