Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Genotype frequency from ped or vcf files
1
gravatar for Ale Lope
16 months ago by
Ale Lope • 10
Ale Lope • 10 wrote:

Hello All,

I would like to get the genotype frequency at each SNP for a specific cohort. I have 2,000 patients divided into three different diseases, so I would like to reproduce the next output (as an example) per each cohort:

          AA  AT  TT   CC  CG  GG

SNP1    .6   .3  .1    -   -   -
SNP2     -    -   -   .2  .5  .3
SNP3     -    -   -   .4  .4  .2
 :
SNPN    .6  .3   .1    -   -   -

I have .ped and vcf files format

Hopefully someone can give me a hint!

Thanks,

Ale
snp geno • 463 views
ADD COMMENT • link •
modified 16 months ago by chrchang523 ♦ 7.7k • written 16 months ago by Ale Lope • 10
3
gravatar for chrchang523
16 months ago by
chrchang523 ♦ 7.7k
United States
chrchang523 ♦ 7.7k wrote:
plink2 --vcf <vcf filename> --geno-counts <column set modifier>

provides counts instead of 0..1 frequencies, but otherwise can report this information in a bunch of ways (see https://www.cog-genomics.org/plink/2.0/formats#gcount for the possible output columns, and https://www.cog-genomics.org/plink/2.0/general_usage#colset for column-set syntax).
ADD COMMENT • link written 16 months ago by chrchang523 ♦ 7.7k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1647 users visited in the last hour
_