bedtools subtract regions within a single file?

[Luke Goodsell]

Hi,

I have a bed file of many overlapping regions, sorted by precedence (in score column). I would like each basepair defined by the file to be present no more than once, assigned to a the lowest value score of any of the regions in the bed file that contain that basepair.

eg:

➜  cat input.bed

chr1 20 30 Region_B 1 +

chr1 10 40 Region_A 2 +

chr1 35 50 Region_C 3 +

should become:

➜  cat output.bed

chr1 20 30 Region_B 1 +

chr1 10 20 Region_A 2 +

chr1 30 40 Region_A 2 +

chr1 40 50 Region_C 3 +

Is there a bedtools way to do this efficiently?

The 'best' solution I have found is:

    touch output.bed;

    while read regionline; do

        echo "$regionline" \

            | subtractBed -a - -b output.bed \

            >> output.bed; \

    done <input.bed

As you would expect, this is very slow.

Many thanks,

Luke

[Aaron Quinlan]

I am sorry, but I can’t think of a clever way to do this solely with bedtools. There may be one, but it don’t easily come to mind for me.

- Aaron

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