Question: How can you sort variants based on their positions from upstream to downstream?
0
gravatar for bioinfo89
6 weeks ago by
bioinfo890
bioinfo890 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 • 151 views
ADD COMMENTlink modified 5 weeks ago • written 6 weeks ago by bioinfo890

Hello bioinfo89,

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

fin swimmer

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by finswimmer1.5k
1
gravatar for Chris Miller
6 weeks ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k 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 6 weeks ago by Chris Miller19k

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 5 weeks ago • written 5 weeks ago by bioinfo890

Please edit your original question with this additional information.

ADD REPLYlink written 5 weeks ago by WouterDeCoster27k

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

fin swimmer

ADD REPLYlink written 5 weeks ago by finswimmer1.5k
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