Question: How can you sort variants based on their positions from upstream to downstream?
0
gravatar for bioinfo89
2.7 years 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 • 674 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years 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 2.7 years ago • written 2.7 years ago by finswimmer14k
1
gravatar for Chris Miller
2.7 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k 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 2.7 years ago by Chris Miller21k

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 2.7 years ago • written 2.7 years ago by bioinfo8940

Please edit your original question with this additional information.

ADD REPLYlink written 2.7 years ago by WouterDeCoster44k

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

fin swimmer

ADD REPLYlink written 2.7 years ago by finswimmer14k
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