NYGC’s cancer pipeline identifies somatic and germline variants from whole genome sequencing (WGS), whole exome sequencing (WES) or targeted panel tumor and normal data. The pipeline can be run on sequencing data from human, mouse and patient-derived xenograft (PDX) models.

Additionally, it can detect microsatellite instability (MSI) and identify mutational signatures within the tumor sample, and predict human leukocyte antigen (HLA) genotypes from the normal sample data.

Pipeline Documentation:

• SomaticPipeline_v6.0_Human_WGS
• SomaticPipeline_v6.0_Human_Exome
• SomaticPipeline_v5B.3

Related Publication:

Arora, K., Shah, M., Johnson, M., Sanghvi, R., Shelton, J., Nagulapalli, K., … Robine, N. (2019). Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms. Scientific reports, 9(1), 19123. doi:10.1038/s41598-019-55636-3.

Variant calls and additional information available on our companion website.