Question: Genome-wide scans for selection using non-model organisms
0
gravatar for aberry814
23 months ago by
aberry81440
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
ADD COMMENTlink written 23 months ago by aberry81440
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2093 users visited in the last hour