Variathon v0.1 - 2013
The goal of this pilot Variation Calling Challenge is to analyze existing or new pipelines for variant calling in terms of accuracy and efficiency. Participants should use their variation calling pipelines on public datasets and they will have the same amount of time to run the tools and collect the results. We provide different simulated data sets for the analysis.
The input consists of a reference genome in fasta format and a set of reads in fastq format from an artificial organism with a genome similar to the reference. The output should be composed of a file containing a table of called variants (e.g., vcf format) and a file with reads mapping (e.g., bam format).
The output will be evaluated in terms of reads mapping, variants calls, and resources usage. Results will be presented at the Workshop on “NGS data and the Variation Calling Challenge” that will be held in May 2013 in Udine, Italy.