1. Genome sequencing alignment and variant calling (PDF)
* Updated (2015) genome sequencing alignment and variant calling practice and solutions, Paper, Supp
2. Tools for subclonal analysis of tumors: ABSOLUTE, SciClone, SubCloneSeeker, CLONET, PyClone, TITAN, CloneHD, CHAT, EXPANDS, PhyloWGS, BitPhylogeny, ClonEvo, SCHISM.
3. GWAS protocols
Basics (in PLOS CB), Guide 1 (full text), Guide 2 (full text), and a Tool (easyGWAS).