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FST Calculation: Resolving -nan Issue in Population Genetics Analysis
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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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Fixation index statistics in Case/Control study - thresholds
written by Lukas •Hi, I am doing data analysis on .vcf file related to case/control study related to schizophrenia humans. For general differenciation between Case/Control groups I picked …
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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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Negative Fst values from VCFtools result
written by nitinra •Hello all, I am calculating Fst using VCFtools and here is the code I am running: vcftools --vcf input.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out pop1_pop2 …
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vcftools --fst-window- problems
written by florycamacho305 •Hi all, I'm using vcftools to calculate fst : vcftools --vcf file.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out pop1_pop2.FST which works. However, when I'm trying to …
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How to pass a variable to vcftools --weir-fst-pop
written by Luther_Blisset •Is it possible to pass a population list as a variable to the `vcftools --weir-fst-pop` function instead of a file? My original code is correct …
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Creating a tree from pairwise FST values for ADMIXTURE components
written by devenvyasADMIXTURE 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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Calculating statistically significant outlier for Pairwise Fst obtained from VCFTools
written by Anurag •Hi, I calculated pairwise Fst using VCFTools: vcftools --vcf input_data.vcf --weir-fst-pop population_1.txt --weir-fst-pop population_2.txt --out pop1_vs_pop2 What method I should use for statistical significance to …
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Vcftools Fst Calculation For Single Snps
written by klimklam •<p>Hi there, I would like to obtain the Weir & Cockerham Fst for single SNPs from my vcf files for wished populations. I thought to …