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Remove multiple gene id from bed file

Hi all,

I have downloaded the bed file from exome analysis from the agilent site. The S33266340_Covered.bed contains multiple entries of gene id (in 4th column) in the same rows. I want only the gene name. what would be the way to remove all entries except gene name in the 4th column?

This is the bed file

browser position chr1:14695-14814
track name="Covered" description="Agilent SureSelect DNA - SureSelectXT HS Human All Exon V8 - Genomic regions covered by probes" color=0,0,128 db=hg19
chr1    14694   14814   ref|WASH7P,ref|NR_024540,ens|ENST00000438504,ens|ENST00000538476,ens|ENST00000488147,ens|ENST00000541675,ens|ENST00000423562
chr1    14928   15048   ref|WASH7P,ref|NR_024540,ens|ENST00000538476,ens|ENST00000438504,ens|ENST00000488147,ens|ENST00000541675,ens|ENST00000423562
chr1    15752   15948   ref|WASH7P,ref|NR_024540,ens|ENST00000538476,ens|ENST00000438504,ens|ENST00000488147,ens|ENST00000541675,ens|ENST00000423562
chr1    16603   17068   ref|WASH7P,ref|NR_024540,ens|ENST00000438504,ens|ENST00000538476,ens|ENST00000488147,ens|ENST00000541675,ens|ENST00000423562
chr1    17235   17421   ref|WASH7P,ref|NR_024540,ens|ENST00000488147,ens|ENST00000438504,ens|ENST00000538476,ens|ENST00000541675,ens|ENST00000423562,miRNA|hsa-miR-6859-
3p
transcript bed genes
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updated by Ram Ram • written by anii • anii

1 answer

Assuming that the gene name in the 4th field is the first field before the ",", then you could use:

awk -F'\t' 'BEGIN {OFS = FS}/^chr/{split($4,a,","); {print $1, $2, $3, a[1]}}' file.bed
• 0 views • link
written by iraun iraun

it works Thankyou

• 0 views • link
written by anii • anii

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