Brian Knaus

The shared library of vcfR currently is rather large. This link, http://dirk.eddelbuettel.com/blog/2017/08/14/#009_compact_shared_libraries, proposes a potential solution.

Create a function to make a site frequency spectrum. Perhaps based off of `genetic_diff()`.

Currently `create.chromR` requires the user to subset the sequence, variant and annotation data to a single chromosome. Some users have expressed that this is overly complex. Adding a parameter `CHROM`...

VCF data may take the form of: POS REF ALT 1110696 A G,T A tidR representation would be: POS REF ALT 1110696 A G 1110696 A T Implementing this, however,...

Add annotation capabilities similar to those found in vcfanno: http://biorxiv.org/content/early/2016/02/29/041863

When the plot method of chromR is called and DP, QUAL, ... etc. are misssing, unexpected results occur. We need to handle this better.

Summarizing variants per sample in a gff/bed type file could allow transfer from vcfR to browsers such as IGV, gbrowse, jbrowse, etc. [Flybase](http://flybase.org/cgi-bin/gbrowse/dmel/) may have a good example from their...

A haploid example dataset could demonstrate the relevance of this software to researchers who study haploid organisms, such as bacteria and true fungi. _Pseudomonas_ may be a good choice.

Allow chrom objects to be subset using [].

If DP is all NA then chromoqc and chromo throws an error. This should be handled more gracifully.