easySFS
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Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
Hi, Isaac! I'm using easySFS, but met the following error .`ModuleNotFoundError:` No module named 'dadi'` I found that it looks like a previous issue #17 So I checked python version....
Hi Isaac! I'm using easySFS to build a site frequency spectrum from a vcf file that was produced with GATK (and edited in VCFtools). It seems that the population of...
The minor allele should be determined based on all populations combined for SFS constructed from more than 2 populations: https://groups.google.com/forum/#!searchin/fastsimcoal/sfs$20multiple$20populations%7Csort:date/fastsimcoal/zWO_ERhHjOg/cnPXsDCXjRAJ EDIT: This is only a problem for unfolded SFS, folded...
Fixed issue (#18 ) of using xrange in python 3 vs 2. Using range makes it compatible for both python 2 and 3. That's all I changed with the code...
plotting is fsck right now. It's a cute trick, so it should work.
Hello, I am trying to use easySFS to generate SFS for 5 populations to be used as input for dadi and fastsimcoal2. I run the following; `vcf=../breeders_noDups_noHighMiss_biallelic_noZ.Jan17-2024.vcf` `id=breedersVcf_IDindpop.txt` `nohup ./easySFS.py...
Hi Issac, I am relatively new to easySFS and SFSs in general! I am attempting to create numerous multidimesional SFSs from 18 different VCF files, all containing 4 different populations....
Hi Issac, I want to produce some plots from the 2D sfs as this important when comparing the models to the empirical data. I also want to view the Fst...
If I am calculating the allele frequency spectrum for a mixed ploidy group from a called VCF file, how should I set the parameters?
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Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis