GENEPOP format input
How to convert genotypes (acgt) to genepop format input? I need to calculate Fst value but POP_dist apliccation does not work
snp
• 1,497 views
•
link
written
by
jessicadorner •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Convert genepop to bayescan format
written by eaabbott0 •Hi all, I'm working with RAD-seq data and have a genepop (.gen) file that I'd like to convert to bayescan format (.geste). I have used …
-
Measure genetic distance between populations (Fst value)
written by jessicadorner •I have problems with the input file for the POP application (measure genetic distance between both populations) in the PEAS program. My file in inp …
-
calculate fst with snp
written by jessicadorner •Do I need to calculate the Fst value for two populations, do you recommend an easy-to-use application?
-
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 …
-
Convert HLA allele to Genepop format
written by setaDear all, I'm trying to used PGDspider tool to convert HLA allele file to Genepop format, however I'm not successful with it. I selected "convert" …
-
Calculate Fst to draw Manhattan plot
written by mostafarafiepourHi All, I trying to calculate Fst. In the first step, I used the following script to calculate Fst with window 100 kb ./vcftools --vcf …
-
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 …
-
Converting Vcftools output to R readable format
written by pifferdavideI have used the following Vcftools code to calculate Fst distances from 1000 Genomes Chr 1 data. c:/path --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf --weir-fst-pop POP1.txt --weir-fst-pop POP2.txt --out …
-
Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
written by kautilyaI want to calculate **markerwise** Weir And Cockerham Fst for certain differentiating markers. I have my data in PLINK(bed/bim/fam) format. I have scourged the internet …
-
Vcf Tools For Fst
written by Tohamy •<p>Dear all, I used VCF tools to calculate Fst between two populations but now I need to calculate pairwise FST between 154 individuals within each …
Please consider investing some effort into your question. One-liners typically do not motivate the community to invest time to help solving your problem. For example, it is unclear in which format you have your data.
[[ Please read before posting a question ::: How To Ask A Good Question ]]
"does not work" is the most uninformative error message => what does not work ::: details!