a modified version of FunSeq2 using new data context
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FunSeq2-1.0_sample_output.tar.gz
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README.md
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funseq2.sh
sample_input.bed
sample_input.vcf

README.md

FunSeq2 Pre-built data context

A modified version of FunSeq2 using new data context

Background

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.

Notes

2017_04_17

  • 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 modifications

  • 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

References

  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).
  2. Khurana, E. et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Sci. 342, 1235587 (2013).
  3. Fu, Y. et al. FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. Genome Biology 15, (2012).