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Compute P-Values for SNP Fst from Pairwise Fst Calculations (--weir-fst-pop)
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Fst Values calculated by 2 different methods were slightly different. Why?
written by kopelol 2Hi, I tried to calculate Fst Values per SNPs using Popgenome(R package) and vcftools, but the value calculated by each methods were slightly different. Do …
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heterozygosity
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Fst Calculation and Visualization
written by safiq713 1Dear all, I am working with ddRAD data, and I have allele and genotype frequencies of different SNPs in different populations. I have calculated Fst …
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Adjusting the Fst values for different sample sizes
written by Siavash Salek Ardestani 2Hi, I calculated the Fst values (through Weir and Cockerham by a sliding-window approach in VCFtools) between two populations with different sample sizes (pop1=32 , …
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Fst with p-values
written by Simo 6Hi all, I've been working with genome-wide data for about 200 samples. I have 150.000 SNPs and I already calculated the Fst using Eigenstrat. I …
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Creating a tree from pairwise FST values for ADMIXTURE components
written by devenvyas 77ADMIXTURE outputs pairwise FST values for all pairs of the components. I know people have generate trees using FST values. I was wondering if anyone …
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How to generate a smoothing plot for Fst along the genome from Lositan output?
written by Anurag 2<p>Hi All,</p> <p>I want to make a genome wide Fst plot using the Lositan output along with P-Values calculated by lositan.</p> <p>Any inputs will be …
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How Do High Fst Compare With Dn/Ds?
written by Adrian Pelin 268<p>Hello,</p> <p>I calculated Fst values for a few genes in my genome pairwise between a couple of isolates.</p> <p>It seems some of the genes have …
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Arlequin Significant Fst Values For Population Sizes N=1, Do Not Match Genodive Fst Values
written by luckylion07 4<p>Hello, </p> <p>I did calculate Fst values with 3 microsatellite makers for 29 populations using Arlequin 3.5.1.3 (Population pairwise Fst values: Compute F-statistics on haplotype …