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Extract strand information from ENSEMBL

I have a set of variants in the following format 

BRAF_7_140453150_A/T  
BRAF_7_140453145_A/T  
BRAF_7_140453145_A/C  
BRAF_7_140453136_A/T  
BRAF_7_140481417_C/A

I want to extract flanking bases for each of this mutation. How do I get the strand information form the above data? I need to create a bed file with the format Chromosome start end strand.

gene snp ensembl
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updated by Emily Emily • written by Gene_MMP8 Gene_MMP8

1 answer

Hello,

I see no reason, why you need the strand information. If I'm correct these list of variants contains all information to create a valid bed file. Assuming that the format is <gene>_<chromosome>_<pos>_<REF>/<ALT> one can use awk:

$ awk -v FS="_" -v OFS="\t" '{print $2, $3-1, $3, $0}' variants.txt > output.bed

If you want to expand the region for e.g. 50bp to the left and right, do this:

$ awk -v FS="_" -v OFS="\t" '{print $2, $3-51, $3+50, $0}' variants.txt > output.bed

fin swimmer

• 1 views • link
written by finswimmer finswimmer

Thanks a lot for your reply. How do I add"chr" to each chromosome number using awk? All my hg19 chromosome numbers are of the form "chr1" etc

• 1 views • link
written by Gene_MMP8 Gene_MMP8

Just add it to the print statement:

print "chr"$2, $3-1, $3, $0
• 1 views • link
written by finswimmer finswimmer

Got it. Thanks a lot

• 1 views • link
written by Gene_MMP8 Gene_MMP8

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