Overview

The long-term goals of the International Sheep Genomics Consortium (ISGC) are to develop underpinning resources for the sheep research community. This has resulted in the continued improvement of the sheep genome assembly and the development of low, medium and high-density Illumina SNP chips. The ISGC members have also made available whole genome sequence data to the community; this has been captured to produce Run3 of the ISGC 1000 genome project. Through the application of a single harmonised pipeline for read QC, mapping, variant detection and annotation, the ISGC makes available variant collections derived in a standardised manner. Run3 has seen ~3500 animals analysed with variant collections positioned on the Rambouillet v2 genome assembly with the aim to provide users with variants defined by chromosomal location, functional annotation, animals of interest, and breeds of interest. In addition to Run3, an alternative to array-based genotyping has been investigated through use of Gencove’s low-pass sequencing plus imputation platform. In order to bring together sequence and array based genotyping results, converting results from SNP chips into VCF format is being investigated.

The historical development of resources is shown below

overview