afplot

Afplot is a little tool to plot allele frequencies in VCF files.

The two main subcommands that are available are:

• regions: Plot single regions or regions from a bed file, optionally with a margin.
• whole-genome: Create a single image for every chromosome on the genome.

Both subcommands have three modes:

• histogram: This will create a histogram with kernel density plot of allele frequencies.
• scatter: Create a scatter plot of allele frequencies, along the region or chromosome.
• distance: Create a scatter plot of distances to theoretical allele frequencies, along the region or chromosome. This only makes sense for autosomes of diploid organisms.

By default, colors correspond to call type (hom_alt/ref/hom_ref).

Multiple VCF files can be supplied simultaneously for the whole-genome subcommand, in which case they can be grouped by label. When multiple VCF files are supplied, plots will be colored on label per VCF file.

Only one sample per VCF file can be plotted.

We currently assume the presence of an AD column in the FORMAT field. This column should contain the depth per allele, with the reference allele being first.

All VCFs should be indexed with tabix, and should contain contigs in the header.

Installation

afplot is available through pypi with: pip install afplot

afplot is also available through conda with: conda install -c bioconda afplot