Human germline small variant calling

We use whole exome (WES) or whole genome sequencing (WGS) data from one or multiple human samples to detect single nucleotide polymorphisms (SNPs) and small insertions and deletions. The variant calling relies on a community-developed pipeline from bcbio-nextgen. The resulting list of variants is first annotated and then filtered based on the predicted effect of the change and the frequency of the variant in the general population.

  • Documentation (download below)
  • Full list of variants (SNPs and indels) with annotations
  • List of protein-changing variants
  • List of variants that are both protein-changing and rare in the general population

 

A zip archive containing the results from an example analysis can be downloaded below . Please refer to the included README and the documentation for more details.