ExAC 0.3.1

[Konrad Karczewski]

Hi ExAC enthusiasts,

We are happy to announce the release of version 0.3.1 of the ExAC data and browser today. This is a minor release of the data, where no sites or frequency data have changed. Since the previous version:

Changes to the VCF:

-Re-annotated with VEP v81 and LOFTEE (v0.2.2)

-Frequency information now broken down by sex

-Some additional variant annotations, described here: ftp://ftp.broadinstitute.org/pub/ExAC_release/current/README.new_annotations

Changes to the browser:

-Read data is now displayed in an IGV web framework

-Constraint information displayed on gene pages (from http://www.ncbi.nlm.nih.gov/pubmed/25086666 and http://biorxiv.org/content/early/2015/10/30/030338)

-LoF annotations from LOFTEE are now displayed on gene and variant pages

-MNP annotations are now displayed on gene and variant pages

-Improved dbSNP search (up to v142)

-Added HGVS nomenclature for splice variants

-Annotations for non-canonical transcript are noted as such on the gene/transcript page

-Many bugfixes, including variant page quality metric graphs

Please feel free to submit any additional issues to https://github.com/konradjk/exac_browser/issues

Additions:

-A number of more nicely formatted tables derived from the VCF, available at ftp://ftp.broadinstitute.org/pub/ExAC_release/current/manuscript_data/

-These can be used to reproduce the figures in the paper using the code at https://github.com/macarthur-lab/exac_2015 (blog post on the process here: http://macarthurlab.org/2016/03/17/reproduce-all-the-figures-a-users-guide-to-exac-part-2/)

Happy exploring,

-Konrad