SNIC
SUPR
SNIC SUPR
Semi-automated WGS pipeline for variant discovery from population sized data
Dnr:

SNIC 2018/3-256

Type:

SNAC Medium

Principal Investigator:

Jennifer Meadows

Affiliation:

Uppsala universitet

Start Date:

2018-05-09

End Date:

2018-12-01

Primary Classification:

30107: Medical Genetics

Allocation

Abstract

*The pipeline has been built, and now requires testing on 10's of individuals to search for bugs. And optimise storage usage. The goal is to develop a semi automated pipeline that would take canine raw fastq and deliver SNP, INDEL and structural variants using a common reference and common program path. At present our collaborative canine group (UU and SLU) has a repository of ~600 WGS, but variants are called using different methodologies and with different thresholds. We seek to harmonize this resource and use our data as a panel of known variation which will in tern, allow us to more easily prioritize trait associated variants for validation and functional assessment. We aim to make our panel of variants a public resource, hosted via UCSC so that all researchers can benefit from this information. The pipeline has been built, and now requires testing on 10's of individuals to search for bugs.