B-map Utilities for VCF

Bvalcalc --Bmap Bmap.csv --positions variants.vcf

--Bmap [path/to/Bmap.csv]

B-map utilities for getting B statistics for specific sites in a VCF/txt file. Provide path to B map as following argument.

Core Arguments

--positions

VCF or two column CSV file [CHR,POS] with list of positions (typically variants) to get B for from the B-map.

Optional Arguments

--plot_distribution [path]

Output path for a plot of the distribution of B across each chromosome (default: B_distribution.png).

--out [path]

Path to save per-site B for variant sites in the VCF/txt file. Results are not saved if --out is not specified.

--out_minimum [float]

Filters positions by B so that only the sites ABOVE the given threshold of B will be returned, i.e. when B >= [out_minimum] is True.

--out_maximum [float]

Filters positions by B so that only the sites BELOW the given threshold of B will be returned, i.e. when B <= [out_maximum] is True.

--quiet

Silence print statements.

Example

Bvalcalc --Bmap Bmap.csv \
  --positions variants.vcf \
  --out variants_B_above_0.9.csv \
  --out_minimum 0.9

This will save a csv file with each position in the VCF with B above or equal 0.9. These variants represent the most neutrally-evolving alleles in the VCF and may be useful for demographic inference, see Demographic Inference with B-map.