This repository defines variant calling challenges using sequence data from the Anopheles gambiae 1000 Genomes Project (Ag1000G).
Details of challenges can be found in the challenges subdirectory.
Submissions are made via a pull request to this repo in the submissions directory of the relevant challenge.
Example submissions are available.
Submissions will be explored and evaluated with results and analyses posted in this repository, which will be a forum for the discussion and improvement of variant calling technologies.
Feel free to open an issue with any questions.
Challenge 1. SNP and indel variant calling from 22 Anopheles gambiae whole genome sequences taken from an experimental cross. Data are short reads from Illumina HiSeq. Submissions evaluated based on Mendelian error rates, and parsimony of inheritance.
Alistair Miles @alimanfoo
Nick Harding @hardingnj
MalariaGEN Resource Centre, Wellcome Sanger Institute, University of Oxford.