popstats

popstats copied to clipboard

Hi, I get a sample size error when I try to execute: python popstats.py --file input --pops POP_CI,POP_SI,POP_AR,POP_TH --ancestor POP_ANC --FAB I have only one ancestral individual. Does the program...

anubhabkhan

Hey, I am have converted my vcf file using the vcf2tped.py script. After that, I want to try to estimate FAB. But when I try to run it using the...

anubhabkhan

Hello, I am using DArTseq data in my analysis. I have missing values and this data type is binary. I was able to upload my data file to Plink and...

Buddhikadahanayaka

About the input files

4

Hi, I am not clear about the input files. For example, I have Pop1, Pop2, Pop3 and Outgroup. I want to calculate D-statistics (Pop1 , Pop2 ; Pop3 , Outgroup)....

guzhongru

Question about 'Dp_main = sum(t_list) / sum(n_list)'

19

Hi Pontus I am trying to run the D-statistics. I followed your suggestion to put the population name in the first column. Then I feed popstats.py with my .tped and...

XueyunF

about h4

1

Dear Pontus, I was trying to understant the parameters for the h4 test (LD option) and I have some doubts the --LD option is the classic D of LD but...

vicbp1

Remove redundant importation of libraries

smlatorreo

Basic question of input files

1

Hi again Pontusk, I was wondering if I use an input that has not not been filtered for Bi-allelic SNPs only will popstats just automatically ignore those SNPs with more...

alx552

--pi not an option

3

Hi, I recently started using your code to estimate f2, since I couldnt seem to get AdmixTools to compile correctly. I have got most of the tests listed in the...

stsmall