Question: Preparing Input data for H12 analysis
0
gravatar for cordeiro.emg
6 months ago by
cordeiro.emg0 wrote:

Dear all,

I am interested in exploring the H12 analysis to detect putative markers under selection using haplotype information. The approach fairly simple and is described in detail in Garud et al (2015). My question is: how can I get my vcf/ped/bed/ files into proper format?

According to the SelectionHapStats documentation in Github, the input file is a line-by-line listing of all the coordinates on the chromosome where there is a polymorphism and the nucleotide states in each individual in the sample

The input file should look something like this:

3948,A,A,A,N,T,A,A,A,T,…etc
7387,A,N,G,G,G,G,G,A,G,…etc
19921,T,G,T,T,T,G,G,T,G,T,…etc
etc..

Using --recode and --transpose flags in plink gives me a similar format, but not quite the same. Any ideas?

Thanks for your help

ADD COMMENTlink modified 6 months ago by RamRS30k • written 6 months ago by cordeiro.emg0

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 6 months ago by RamRS30k

Did you figure this out? I'm having the same issue.

ADD REPLYlink written 5 weeks ago by shendri40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1055 users visited in the last hour