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hammerlab / variant-calling-benchmarks

Automated and curated variant calling benchmarks for Guacamole
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A somatic reference standard for cancer genome sequencing #39

Open arahuja opened 7 years ago

arahuja commented 7 years ago

http://www.nature.com/articles/srep24607

performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions.

common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

All BAMs and VCFs, including that for the final somatic reference, can be accessed through NCBI’s (National Center for Biotechnology Information) dbGaP (database of Genotypes and Phenotypes; accession number phs000932) and the European Bioinformatics Institute (EGA (European Genome-phenome Archive) accession number EGAS00001001385).