A modified version of FunSeq2 using new data context
FunSeq2 is a tool to prioritize and annotate somatic variants from cancer whole genome sequencing. It uses a pre-built data context, which is generated from different genomic and cancer resources and updated on regular basis. We provide latest FunSeq2 scripts (with bug fixes) and updated data context.
- FunSeq2_DC3 refers to FunSeq2 pre-built data context 3. It contains PCAWG OCT-2016 annotations
- FunSeq2_DC2 refers to FunSeq2 pre-built data context 2. It contains PCAWG OCT-2015 annotations
- FunSeq2-1.0 refers to the original published work by Fu et al, 2012
Pre-built data context sources
- FunSeq2_DC3 (http://khuranalab.med.cornell.edu/data_DC3.html)
- FunSeq2_DC2 (http://khuranalab.med.cornell.edu/data.html)
- FunSeq2-1.0 (http://funseq2.gersteinlab.org/data/2.1.0)(http://khuranalab.med.cornell.edu/data.html)
- Fix new spliceOverlap annotations from VAT
- Map current terms to sequence ontology terms
- splice_variant means either splice_donor or splice_receptor
- Change enhancer annotations to include tissue-specificity
- code is modified to incorporate specific format.
- Remove hierarchy and annotate all
- Do not remove germline
- MAF=1
- Dhingra, P., Fu, Y., Gerstein, M. & Khurana, E. Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization. Curr. Protoc. Bioinforma. 57, 15.11.1-15.11.17 (2017).
- Khurana, E. et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Sci. 342, 1235587 (2013).
- Fu, Y. et al. FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. Genome Biology 15, (2012).