usage: vcf_to_LDhat_genotype.py [-h] vcf bed Nsnps chr Nwin

Description: Take a gzipped VCF file as an input, the region and the number of
SNPs to extract from VCF and outputs the LDhat inputs, the sites and locs files.

sites file
4 10 2
>GenotypeA
122110?000
>GenotypeB
1111201100
>GenotypeC
011111?112
>GenotypeD
2112210100

locs file
10 1200 L
1 57 180 187 223 250 438 509 878 1034

For genotype/unphased data, the convention used is 0 and 1 for the two
homozygotes, and 2 for heterozygotes. ? is used for missing data. The first line of the
sites file is as follows: 4: number of sequences, 10: number of SNPs, 2: unphased
The first line of the locs file is as follows: 10: number of SNPs, 1200: total
length of the sequence, L: using cross-over model (the other model is the gene
coversion model)

It then processes the Ldhat outputs to produce plots and dataframes needed for downstream
analysis.

positional arguments:
vcf gzipped VCF
bed scaffold length file in bed format
Nsnps number of SNPs
chr chromosome or scaffold
Nwin number of windows

optional arguments:
-h, --help show this help message and exit