Where to start - for noobies

http://online-learning.harvard.edu/series/xseries-data-analysis

Coalescence

Fast intro

http://www.popgen.wzw.tum.de/fileadmin/pdf/Tellier-Lecture3-Coalescent-Mutations-EffectPopSize.pdf

Classic papers

Hudson - Gene genealogies and the coalescent process

http://home.uchicago.edu/rhudson1/popgen356/OxfordSurveysEvolBiol7_1-44.pdf

ANGST

Intro

https://cgrlucb.wikispaces.com/file/view/CGRL_SNP_workshop.pdf

fST

Nucleotide diversity

https://github.com/mfumagalli/ngsTools/blob/master/TUTORIAL.md

http://www.popgen.dk/angsd/index.php/Heterozygosity

SNP filters

http://www.popgen.dk/angsd/index.php/Filters

Heterozygosity

http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests

SFS

https://github.com/ANGSD/angsd/wiki/SFS

SFS - theory

https://math.la.asu.edu/~jtaylor/teaching/Spring2017/BIO545/lectures/frequencies.pdf

ABBA

http://www.popgen.dk/angsd/index.php/Abbababa

Watterson thetha

https://www.biostars.org/p/150600/

https://www.biostars.org/p/178983/

PLINK

ROH

http://zzz.bwh.harvard.edu/plink/ibdibs.shtml#homo

Raxml tree making

Generate A Tree With Bootstrap

https://www.biostars.org/p/73678/

Variant Calling

General pipeline and trutorial

http://cbsu.tc.cornell.edu/lab/doc/variant_workshop_part2.pdf

https://gencore.bio.nyu.edu/tag/gatk/

GATK tutorial

https://qcb.ucla.edu/wp-content/uploads/sites/14/2016/03/IntroductiontoVariantCallsetEvaluationandFilteringTutorialAppendix-LA2016.pdf

Best Practices - how to apply hard filters

https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set

Best Practices - VQSR

https://gatkforums.broadinstitute.org/gatk/discussion/comment/32399

Multi-sample calling

https://gatkforums.broadinstitute.org/gatk/discussion/2776/multi-sample-calling-vs-single-sample-calling

Visualize it!

https://software.broadinstitute.org/gatk/documentation/article.php?id=6925 http://mbontrager.org/blog/2016/08/17/Variant-Exploration

BEAST

trouble shooting

https://taming-the-beast.github.io/tutorials/Troubleshooting/Troubleshooting.pdf

tip dating

https://www.biostat.washington.edu/sites/default/files/modules//2016_SISMID_13_11.pdf

LaTeX

R Markdown

https://www.datacamp.com/courses/reporting-with-r-markdown/

notebooks

https://www.rstudio.com/resources/webinars/introducing-notebooks-with-r-markdown/

MySQL

get Genome Browser to work via mysql

https://www.biostars.org/p/4544/