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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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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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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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per site max fst and avg fst within windows?
written by mrfz003 •I 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 setaHi 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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Fst value inflation in BayeScan?
written by aesculus •I am testing several RADseq SNP datasets for Fst outliers using BayeScan 2.1. These datasets represent the same sampling of individuals, but with different numbers …
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Indel heterozygosity frequency
written by hdtms •Hi 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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how to assign kmer value for paired end reads
written by girijakaushal •Hello I am trying to find optimal kmer value using kmergenie so as to use that kmer value in Metavelevet tool for metagenome assembly. Q. …
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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 …