Question: Allele frequency for chr3 variants in 90 random YRI samples from 1000Gp3
gravatar for iaguilaror
4.1 years ago by
iaguilaror0 wrote:

Hi. I've used Biostars before but this is my first time posting. I'm complete novice in genomics and programming, but I learn fast. Hope you can help me with the following problem.

My PI gave me a file with the following format:


3 401373 C T 0.0483870967741935

3 534104 A G 0.0591397849462366*

The file records single nucleotide variants in chromosome 3, where AF indicates allele frequency in our study population (90 individuals). What I need is a similar file but for 90 random individuals from the YRI population in the One Thousand Genomes Project.

From the 1000Gp data portal I have downloaded a list of 111 sample names that meet my needs. I already picked 90 random sample names in this format:

*Sample name Sex Biosample ID Population code Population name ...

NA18853 male SAME124733 YRI Yoruba ...*

My question is: how do I create a file that reports Chr POS REF ALT AF just for the samples (population slice) in the list.

Thanks in advance.

ADD COMMENTlink modified 4.1 years ago by Denise - Open Targets5.1k • written 4.1 years ago by iaguilaror0
gravatar for Denise - Open Targets
4.1 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.1k wrote:

Have a look at the Allele Frequency Calculator.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Denise - Open Targets5.1k
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