Question: Genome-wide scans for selection using non-model organisms
gravatar for aberry814
23 months ago by
United States
aberry81440 wrote:

I have un-phased genome-wide SNP data from 150 samples of a diploid, non-model organism representing a single population. I am looking for a pipeline that will allow me to perform tests of selection across the genome, looking for regions that exhibit patterns of positive or purifying selection. I am imagining a test like an integrated haplotype score (iHS) that I could graph with genome position on the X-axis and the iHS statistic on the Y-axis and look for deviations from zero. There are several pipelines that exist, but all seem to be difficult/impossible to adapt to any organism other than human (i.e. SHAPEIT which requires chromosome mapping files, and ancestral state reconstruction). All I have is the fasta file (supercontig assembly, not chromosome) of the reference I used for genome assembly, a VCF file with SNPs, and consensus sequences for each of my samples (using ambiguity codes for heterozygous sites).

Does anyone have any experience doing such a genome scan for selection with a non-model organism? Or even accurately estimating the phase (which is the first step)?

snp plink natural selection • 728 views
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