Question: How can you sort variants based on their positions from upstream to downstream?
0
gravatar for bioinfo89
10 months ago by
bioinfo8940
bioinfo8940 wrote:

Hello!

I have a set of variants with coding sequence positions for eg:

c.-3A>C

c.134+1G>A

c.*5362T>C

~10,000 of such variants in a single file.

Aim: I want to sort them based on their position from upstream to downstream of the gene (5'UTR variants followed by coding region and then followed by 3' UTR variants).

Is there any method or a tool available which can do this?

Any help will be appreciated!

snp • 343 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by bioinfo8940

Hello bioinfo89,

does your file realy just contains this variant description? What about the gene and transcript informations?

fin swimmer

ADD REPLYlink modified 10 months ago • written 10 months ago by finswimmer8.9k
1
gravatar for Chris Miller
10 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

You really need to provide more information on what kind of file format you have, but for shits and giggles, let's assume it's a bed file with the first three columns: chromsome, start, stop. Sorting is then as easy as:

sort -k 1,1 -k 2,2n myfile >outfile
ADD COMMENTlink written 10 months ago by Chris Miller20k

Oh yes I should have mentioned this before, I have coding sequence positions for the variants eg. c.-3A>C, c.134+1G>A, c.*5362T>C.

ADD REPLYlink modified 10 months ago • written 10 months ago by bioinfo8940

Please edit your original question with this additional information.

ADD REPLYlink written 10 months ago by WouterDeCoster35k

These are still not enough informations. Please post the first lines of you file.

fin swimmer

ADD REPLYlink written 10 months ago by finswimmer8.9k
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