Fst calculation between my own population and 1000 genome populations

Question

[seta]

Hi all and Merry Christmas!

I would like to calculate Fst for some selected SNPs between my own population (the variants came from whole-genome sequencing of about 800 individuals) and other populations in 1000 genome. To this end, I extracted the variants of interest using VCFtools with --recode --keep-INFO-all in the command from each chromosome VCF file, then I concatenated all extracted vcf files using bcftools to have the single vcf file with all chromosomes within it. So, now, I have the single vcf file containing variants of interest in all chromosomes from my population and another similar file from 1000 genome. Now, for calculating Fst between my population and 1000 genome population, these two files should be merged, yes? or is there a possibility to calculate Fst between two separate vcf file? However, I am not sure how they should be appropriately merged for Fst calculation by the available tools, say vcftools. Please share me your suggestions and comments.

Thank you in advance

Answer 1

[cetin.m]

When I did something similar I used a python code which did not involve merging the files.

[seta]

I wanted use vcftools for fst calculation, I merged vcf files using bcftools, but couldn't successfully calculate fst on the merged vcf file. Could you please share your script?

[shreyajha]

Hi.. Even I would like to have your script. It would be really great if you could share'

Thanks in Advance.