In this Repo

• raw: Raw data
• qc: Scripts for quality control
• eig: Eigenanalysis/PCA and further quality control
  • CONVERTF: Preparation of input files for eigenanalysis
  • EIGENSTRAT: Eigenanalysis/popstruct
  • POPGEN: PCA/Fst (Hudson)
• ibd: Identity by descent computation
• ihs: Selection scan by the integrated haplotype score
• fst: Wier-Cockeham (WC)
• ld: Linkage disequilibrium (LD) analysis
• hflk: Selection scan by the extended Lewontin-Krakauer Fst outlier test (FLK) and its haplotype variant hapFLK
• sample: Sample files
• maf: Minor allele frequency analysis
• lroh: Long runs of homozygosity
• recomb: Fine-scale recombination map computation
• fws: Complexity/Multiplicity of infection (for Plasmodium parasite analysis)

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Many of the packages used to perform various analyses are not available for either the default python installation (2 or 3) or R version. Therefore, several anaconda environments were created to handle package incompatibility issues. Below are yml files for the environments used to handle all packges necessary to perform all analyses in this repo.

• R.yml
• R2.yml
• R3.yml
• eigen.yml
• py2.yml
• py3.yml

Create identical env from the yml files

conda env create -f [].yml 

General Usage

Pre-processing of raw data (/raw)

Merge single chromosomes into one file

./mergeVCFs.sh <file> <output>

Update chromosome and snp IDs so that plink does not spill out errors

./updateIDs.sh <merged-vcf>

Extract data for analysis as outlined above (For parasite analysis)

./extract_data.sh <updated-vcf>

Quality Control (/qc)

Run qc pipeline

./qc-pipeline

PCA (/eig)

/CONVERTF

./convertf_all.sh

/EIGENSTRAT

./run_eigenstrat.perl

/POPGEN

./run_popgenstats.sh

iHS (/ihs)

Convert phased haplotypes in VCF to rehh format (.hap+.map)

./phased_vcf2rehh.sh -h 

Get help for using the script by typing '-h' on the commandline

Run scan for selection

./runScan.sh

Just hit 'enter' and the script will guide you through

Resources

• karyoploteR: https://bernatgel.github.io/karyoploter_tutorial/
• SMCPP: https://github.com/popgenmethods/smcpp
• PSMC: https://github.com/lh3/psmc
• ASMC: https://www.palamaralab.org/software/ASMC#tools
• LocusZoom: https://github.com/statgen/locuszoom
• DataViz: https://paldhous.github.io/ucb/2015/dataviz/week7.html
• Polygenic adaptation: https://figshare.com/articles/Code_and_metadata_Genetic_architecture_and_selective_sweeps_after_polygenic_adaptation_to_distant_trait_optima/6179219
• ClassifyCNV: https://github.com/Genotek/ClassifyCNV
• VPOT: https://github.com/VCCRI/VPOT/
• DNAscan: https://github.com/KHP-Informatics/DNAscan
• Browning Lab Beagle Utilities: https://faculty.washington.edu/browning/beagle_utilities/utilities.html
• ABC: https://cran.r-project.org/web/packages/abc/index.html
• ARGweaver (ancestral recomb graph): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022496/
• Balancing selection: https://github.com/ksiewert/BetaScan
• Calculating selection: https://www.ucl.ac.uk/~ucbhdjm/courses/b242/MaintVar/MaintVar.html
• pyrho (demography-aware ancestral recombination graph): https://github.com/popgenmethods/pyrho
• mutation dating paper: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000586
• mtDNA Evolution: https://academic.oup.com/mbe/article/17/6/951/1037844
• NCBI HAPMAP: https://ftp.ncbi.nlm.nih.gov/hapmap/
• ENSEMBL FTP (GRCh37): http://ftp.ensembl.org/pub/grch37/release-104/gff3/homo_sapiens/
• CODEML: Inference of Episodic Changes in Natural Selection Acting on Protein Coding Sequences via CODEML (https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpbi.2)
• PAML: Detecting the Signatures of Adaptive Evolution in Protein-Coding Genes (https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471142727.mb1901s101)