How to calculate SNP frequency for each population in bfile using plink?
0
0
Entering edit mode
3 months ago
Rudra • 0

I want to calculate frequency of a SNP for each population in bfile using plink...Please help..!!Thanks in advance

Frequency • 235 views
ADD COMMENT
0
Entering edit mode

What have you tried?

ADD REPLY
0
Entering edit mode

I have tried plink --bfile data --freq --out freq

ADD REPLY
1
Entering edit mode

Always mention what you need, what you have tried, what you get from your trials and how this differs from what you need. Outlining the above will help you and others solve your problem quickly.

ADD REPLY
0
Entering edit mode

above command give overall frequency, i want frequency for each population separately..

ADD REPLY
0
Entering edit mode

How are you incorporating the sample to population mapping? Imagine an Excel spreadsheet with variants in each row and samples in each column. Where is the information that gives you the population identifier given the sample identifier?

ADD REPLY

Login before adding your answer.

Traffic: 1991 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6