Tool: Quick Command to Filter Bam Files
Hi,
Was looking for a while on how to edit bed files to specific chromosome regions which made sense to me. Finally made this quick AWK command that made the outcome simple:
awk '{if ($2>=START_COORDINATES && $3=<END_COORDINATES && $1=="CHROMOSOME") print $1, $2, $3}' file.bed > file_mod.bed
An example with the command would be:
awk '{if ($2>200 && $3 <300 && $1=="chr10") print $1, $2, $3}' file.bed > file_mod.bed
Cheers.
P.S. also - check out Pierre's suggestion below!
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Your example requires full containment, in that both start and end are within the interval, whereas the solution by Pierre Lindenbaum solution accepts any overlap.
Though I think there might be a subtle bug there, since in BED format one coordinate is inclusive while the other not, it feels that one check should have
>=I'd rather use bedtools intersect (or bedops intersect/element-of) than mess around with
awk. More performant and better documented, easier to read.Great suggestions!