You can use e.g. R and the seqminer-Package (https://cran.r-project.org/web/packages/seqminer/index.html) to read VCF-files and create a data matrix.

If you are going to program the PIC calculation yourself in R, Annette has the best answer.

If you want some other software to calculate PIC for you, what format of binary data matrix is that software asking for? Does it allow the plink binary format as input, which is fairly common?

I'm refering to the binary format indicated in the PIC calculator online : http://w3.georgikon.hu/pic/english/kodom.aspx

how do I generate such a file from my vcf file

I don' think there is a easy way to re-format your VCF file into the one required by the online calculator. The format is not good, and no documentation about that format is there.

But, since what you have are SNPs, they should all be bi-allelic. For a bi-allelic SNP, it is not hard to calculate its H and PIC values according to the paper attached to that

online calculator.

H = 1 - p^2 - (1-p)^2, and

PIC = H - 2 * p^2(1-p)^2

where p is the frequency of one of the two alleles, and since the SNP is bi-allelic, (1-p) is the frequency of the other allele.

You have thousands of SNPs, you can use plink to calculate the allele frequency p for all of them, but first you need to transfrom the VCF file into

Plink binary format.

##1. Download plink1.9 from https://www.cog-genomics.org/plink2, unzip it, copy plink (or plink.exe if you use windows) into your working directory, your VCF file should also be moved or copied here.

##2. convert the VCF file, say it is named "your.vcf" (or "your.vcf.gz" if it is compressed) into the binary plink BED format (a triplet of *.fam, *.bim and *.bed)

./plink(.exe) --vcf your.vcf(.gz) --make-bed --out matrix

## matrix.fam, matrix.bim and matrix.bed should appear in your working directory

##3. Use plink again to calculate allele frequency p for all the SNPs:

./plink(.exe) --bfile matrix --freq --out your

## your.frq should appear in your working directory

You can use excel to open "your.frq", it is a space delimited table, with each row recording one SNP.

The column "MAF" is the allele frequency p you needed.

You can calculate H and PIC for all the SNPs in excel, using the two formulas.

https://www.cog-genomics.org/plink2

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