leahkemp/test_SV_callers

Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human).

Test structural variant (SV) callers

General info

This relates to the Genomics Aotearoa clinical genomics project undertaken by the human genomics group at ESR. Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human) and figuring out how to ingest the SV vcf files into scout.

Raw data location

• The raw data for this project is stored/backed up at /NGS/clinicalgenomics/archive/2022/results/GA_clinical_genomics/wellington/phase_2/bams/ on ESR's production network

Analysis location

• This analysis was for the most part carried out at /NGS/scratch/KSCBIOM/HumanGenomics/test_SV_callers/ on ESR's production network
• A minimal version of the analyses were stored/backed up at /NGS/clinicalgenomics/archive/2022/results/test_SV_callers/ on ESR's production network

Analysis workflow for reproducing this analysis

• 01 - Assumptions
• 02 - Setup
• 03 - Test manta
• 04 - Compare vcf
• 05 - Clean up

Access

• The github repository for this project is public
• For other general queries about this project beyond the bioinformatics, contact the current (2022) representatives of the ESR genomics group, Donia Macartney-Coxson (Donia.Macartney-Coxson@esr.cri.nz) and/or Joep de Ligt (joep.deligt@esr.cri.nz)

Github repository

Find the github repository for this project at: https://github.com/leahkemp/test_SV_callers

Results webpage

No results webpage