Single VCF on a single region

• afplot regions histogram -v my.vcf.gz -o output_dir -R chr1:100-200

Single VCF on a bed file

• afplot regions histogram -v my.vcf.gz -o output_dir -L regions.bed

Single VCF whole genome

• afplot whole-genome histogram -v my.vcf.gz -l my_label -s my_sample -o mysample.histogram.png

Multiple VCFs whole genome

• afplot whole-genome histogram -v my1.vcf.gz -l my_label1 -s my_sample1 -v my2.vcf.gz -l my_label2 -s my_sample2 -o both_samples.histogram.png

Grouping samples can be achieved by supplying identical labels to samples. E.g.

• afplot whole-genome histogram -v 1.vcf.gz -v 2.vcf.gz -v 3.vcf.gz -v 4.vcf.gz -l group1 -l group1 -l group2 -l group2 [...]

Excluding contigs on whole genome

In certain cases, you may not want to plot all contigs. For instance, when your vcf header contains many small unplaced contigs. This can be achieved by supplying a regex pattern to the -e flag. For instance, all contigs containing “gl” can be filtered out by doing:

• afplot whole-genome [...] -e '.*gl.*'

0.2

The entire command line interface was changed to use click, instead of regular argparse. This allows a more complex CLI. In stead of having flags for plot mode, afplot now uses subcommands.

While the CLI has changed, and the internals of afplot have been refactored, the old-style (version 0.1) API remains in place for now. This may be deprecated in the future.

Support for plotting regions was added. Region plotting outputs on a directory, rather than on a single file.