genewise-tSNE

Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae. Data set from Anopheles gambiae 1,000 Genomes Project phase 1. https://www.malariagen.net/projects/ag1000

Variant calling files preparation

• gene-extractor.pl : Extract individual VCF files for each gene or window;
• filter_SNPs.sh : Select exonic SNPs;

Gene by gene PCA plotting, distance matrix and other metrics

• metrics.sh & metrics2.sh : Check VCF metrics such as: missing data, SNP frequency, number of SNPs, nucleotide diversity, etc.
• genewise-Fst.R : Calculate Fst between M and S forms for each gene;
• genewise-PCA.R : Perform a principal component analysis for each gene and convert to VCF to GDS;
• genewise-dist.R : Perform distance matrix for each gene;

Linearize matrices and big table format

• bigtab-create.R : Create the big table with all linearized values for each gene;
• bigtab-PCA.R : PCA of big table created;
• bigtab-tSNE.R: tSNE of PCs.

Plotting in R

• bigtab-tSNE-plot.R : plot for figure 2;

DBScan

• per-chro-DBScan.R : Performe DBScan for collinear regions of each chromosome arm (2L example).

Web Interface

• Directory : shiny