calculate fst for every allele in any position
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16 months ago

Hi Dear all,

I have a table of SNPs with alleles in any position (alleles A1 and A2) (As you can see in the table below). So, I want to calculate the Fst for each position. I can only calculate Fct for the VCF file but I have no idea about it.

What is the best idea?

SNP              Chr    Position   A1   A2
AX-85070764       0     52193      G    A
AX-85125208       0     76511      A    G
AX-85102691       0     97615      G    T
AX-85160125       0     116502     C    A
AX-85127001       0     254208     C    T
AX-85119002       0     307773     A    G
AX-85069970       0     372522     T    C
AX-85059862       0     464239     T    C
AX-85112924       0     496560     G    A
AX-85104270       0     738126     G    A
AX-85091977       0     911657     A    G
AX-85058183       0     949512     A    G
AX-85078603       0     984527     T    C

SNP Fst • 341 views