How to calculate SNP frequency for each population in bfile using plink?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Computing allele frequencies per individual for a set of SNPs in PLINK
written by pifferdavide
-
Calculating polygenic score using plink
written by m.shoaib •
-
Selection of random SNPs with similar allele frequency with my SNPs under study
written by seta
-
How to calculate Minor Allele Frequency (MAF) for your own population data
written by Sudhir Jadhao
-
Missing Rate within arrays
written by vgenepi •
-
Plink Family Structure/Population stratification
written by Tom •
-
Minor allele frequency calculation
written by Tark •
-
Accounting for problem SNPS when merging multiple plink files
written by lhvkl •
-
Getting Population Specific Allele Frequency For Illumina Genotyping Data
written by yling1 •
-
How To Calculate All Ld Results For 1000G Raw Genotypes?
written by J.F.Jiang
What have you tried?
I have tried
plink --bfile data --freq --out freqAlways 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.
above command give overall frequency, i want frequency for each population separately..
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?