Somatic-Variant-Calling

This repo will sumarize state of art variant calling methods

Somatic variant calling

Somatic Wrapper

https://github.com/ding-lab/somaticwrapper

TinJasmine

https://github.com/ding-lab/TinJasmine

Germeline variant calling

GermlineWrapper

https://github.com/ding-lab/GermlineWrapper.workflow

TinDaisy

https://github.com/ding-lab/TinDaisy

DNA and RNA alignment

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. https://www.nature.com/articles/s41587-019-0201-4#code-availability https://github.com/DaehwanKimLab/hisat2 http://daehwankimlab.github.io/hisat2/ https://anaconda.org/bioconda/hisat2

Which Aligner Software is the Best for Our Study?

https://www.clinmedjournals.org/articles/jggr/journal-of-genetics-and-genome-research-jggr-7-048.pdf

investigating the direct impact of variants on protein structure

Hotspot3D https://www.nature.com/articles/ng.3586