How can you sort variants based on their positions from upstream to downstream?

Question

[bioinfo89]

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!

[finswimmer]

Hello bioinfo89,

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

fin swimmer

Answer 1

[Chris Miller]

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

[bioinfo89]

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.

[WouterDeCoster]

Please edit your original question with this additional information.

[finswimmer]

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

fin swimmer