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Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
written by S •I'm getting different Fst values when I use `vcftools --weir-fst-pop` vs. the `varcomp.glob()` function from the R `hierfstats` package. I'm not sure why because they …
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Calculating weir-fst by vcftools
written by Liangfa •Hi, I'm using vcftools to calculate weir-fst, and getting confused by the result. One of the records is below, two populations, subpop1 and subpop2. I'm …
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manhattan plot
written by anithanagaraj93 •I calculated fst values by using following command, "vcftools --vcf a.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out ex" and got negative and -nan Fst values. if …
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Calculating Fst from low coverage data using genotype likelihoods
written by JautisHello, I have low coverage (~1x) sequencing data from ~50 individuals from two populations and would like to calculate Fst for each biallelic variant. I …
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Pairwise Fst values derived from different algorithms?
written by giulia.trauzzi •Hello, I know that the Wright's Fixation Index (Fst) can range between 0 and 1 and for pairwise Fst is the same meaning that 0 …
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Adjusting the Fst values for different sample sizes
written by Siavash Salek Ardestani •Hi, 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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How to detect outliers from either (a) SNP-Fst or (b) Window-Fst distributions?
written by serpalma.v •Hello I want to find the SNPs that could be responsible for the phenotype differences observed between three populations. For that I computed Fst (weir …
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Calculating Fst from simulations
written by Rubal<p>Hi All,</p> <p>I calculated Weir and Cockerham's Fst using VCF tools and want to use simulations to have a feeling whether my high Fst regions …
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Fst Across Several Population
written by thjnant<p>Hello, </p> <p>Concerning Weir and Cockerham 1984 Fst, I can understand it when we set r = 2 which is a comparison between two populations. …
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Weir-Fst Vcftools
written by thjnant<p>Hello, </p> <p>I am using the weir-fst in vcftools to calculate the pairwise fst. I have also written my own script using the Weir and …
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