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Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
written by S 1I'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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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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manhattan plot
written by anithanagaraj93 2I 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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Negative Fst values from VCFtools result
written by nitinra 5Hello 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 0Hi 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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per site max fst and avg fst within windows?
written by mrfz003 0I have SNP data in VCF format as well as a gtf file with defined positions for genes. Does anyone know of a quick way …
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How vcftools calculate Fst value?
written by seta 191Hi all, I used vcftools for calculation the Fst value between two populations (pop1 and pop2) using the below command: ./vcftools --vcf file.vcf --weir-fst-pop population_1.txt …
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Indel heterozygosity frequency
written by hdtms 2Hi I'm working with Indels filtered using GATK best practices, I got a vcf, converted to plink and calculated the heterozygosity frequency using plink function …
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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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Weir-Fst Vcftools
written by thjnant 16<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 …