Tier 2 project discovering genomic patterns of introgression across the Karimata Strait
Variant calling: SNPArcher (https://github.com/harvardinformatics/snpArcher)
Data filtering and PCA: PLINK (https://www.cog-genomics.org/plink/1.9/), PLINK2 (https://www.cog-genomics.org/plink/2.0/), vcftools (https://vcftools.sourceforge.net/), and bcftools (https://samtools.github.io/bcftools/bcftools.html).
Population genetic clustring: ADMIXTURE (https://dalexander.github.io/admixture/download.html)
Nucleotide diversity, Fst and Pixy: Pixy (https://pixy.readthedocs.io/en/latest/installation.html)
As Pixy requires python between 3.6 and 3.7, whereas SNPArcher uses 3.11, we need to create two conda environments for the program installations.
In this project, we sampled multiple small vertebrate species (abbreviations used across the analyses):
Hose's frog, Odorrana hosii (OH)
Genus Chalcorana (CH)
Whitehead's spiny rat, Maxomys whiteheadi (MW)
Many-lined sun skink, Eutropis multifasciata (EM)
......
For each species, we:
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called genomic variants (SNPArcher, configuration folder as "config" and script to proceed as "XX.sh").
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filtered SNP, scanned genomic landscape, and ran PCA and ADMIXTURE ("XX_p_script.sh", "remove.txt", "XX_popfile.txt").
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plotted pi, Fst, and Dxy across the genomic landscape ("vis.R")