最新的肿瘤数据分析方案

Version 2 of the PROSIC caller for somatic variants.

https://github.com/PROSIC/prosic2

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

https://github.com/cancerit/CaVEMan

A tool to call somatic single nucleotide variants.

https://github.com/genome/somatic-sniper

An ensemble approach to accurately detect somatic mutations using SomaticSeq

https://github.com/bioinform/somaticseq

Microassembly based somatic variant caller for NGS data

https://github.com/nygenome/lancet

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

https://github.com/mskcc/facets

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

https://github.com/broadinstitute/ichorCNA

A pipeline for processing tumor normal WES data with VarScan2.

https://github.com/dkdeconti/DFCI-CCCB-TumorNormalPair-WES-pipeline

肿瘤自动化报告方案

github地址:

https://github.com/sigven/pcgr

文章地址:

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btx817/4764004

demo报告:

http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.3.pcgr.html

TMB:

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