BED file modification

Question

[adarsh_pp]

Hello,

I have BED file with all the chromosome coordinates.

I need to remove ChrX, ChrY and ChrM from this file.

Please suggest how this can be done.

Thanks

[Victor J. Fernández]

Hello,

The toolkit Bedops is very useful. Here you can see how to extract a specific chromosome with the utility "bedextract".

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedextract.html

Answer 1

[Pierre Lindenbaum]

awk '(!($1=="ChrX" || $1=="ChrY" || $1=="ChrM"))' in.bed