Conversion of vcf file.

Question

[christina-v7]

Hey everyone,

I am pretty new when it comes to bioinformatics and to the site as well. But I really need some help. I' m sorry if my question is kind of stupid. I was given for an assignment a vcf file that it contains the polymorphisms that have been found at a part of a chromosome. I am asked to convert the vcf file to an ms output. I've tried some things but I am not sure if the results are correct. Does enyone have an idea of how we do it?

Thanks in advance!

[WouterDeCoster]

an ms output

A what?

[christina-v7]

Ms is a program we use to generate samples under a variety of neutral models. And we are asked to use the vcf file to create an output with the ms program.

[GenoMax]

If that is a publicly available/accessible program then please provide a link for it in the original question.

[h.mon]

I guess she is talking about this ms:

http://home.uchicago.edu/~rhudson1/source/mksamples.html

[WouterDeCoster]

Have you considered telling us how that file looks like?

[h.mon]

If I am guessing correctly the ms software she is referring to, you won't like the file format:

ms 4 2 -t 5.0
27473 36154 10290
//
segsites: 4
positions: 0.0110 0.0765 0.6557 0.7571
0010
0100
0000
1001
//
segsites: 5
positions: 0.0491 0.2443 0.2923 0.5984 0.8312
00001
00000
00010
11110

The explanation of the format can be found at the manual, which can be found following the link I provided to genomax.

[WouterDeCoster]

I confirm your suspicions with regard to not-liking the format.

I just think that it's unfair that christina-v7 expect us to google for the format and dig for the manual, to figure out the file format that OP wants. I'd prefer some more effort here.

[christina-v7]

Yeah,you are right.And I'm really sorry. But yesterday something came up and I did not have time to reply. I'm really sorry and thank you for your efforts to find what I was talking about.

[christina-v7]

Yeah that is what I was referring to. If you need me to send something else please tell me.

[peter]

Hi @Christina-v7 I am trying to achieve that as well. Did you find a way to do it?