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Allele frequency for chr3 variants in 90 random YRI samples from 1000Gp3

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:

*Chr POS REF ALT AF

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.

snp 1000gp3 data access population genetics

1 answer

Have a look at the Allele Frequency Calculator.

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