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ndeshpan 05-16-2016 11:25 PM

GATK multisample vcf to BayeScan input
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Hi all,

I am trying to convert a "multi-sample (population)" vcf file from GATK obtained using a "joint genotyping workflow" for a non-model organism. Since we want to do population studies, I need to convert the .vcf file to a format used as input to a tool such as BayeScan (

I tried using file conversion tools such as PGDSpider "". which gives me an output but for only for the 1st sample (population) !!!

I am attaching my input and output files for reference..

Appreciate any feedback,



Any other tools to do Fst outlier analysis using a "vcf" file with multiple samples?

alexbenroland 03-23-2017 11:27 AM

Hi Nandan,

I hope you fixed your problem since that time.
Anyway, I think you need to convert your file in the PGDSpider own format (PGD), then concert to Bayescan format. I was having the same problem of conversion for different input format type, and it was resolved that way.

In short, convert that way in 2 steps:
VCF -> PGD -> Bayescan


Gopo 03-24-2017 07:34 AM

PGDSpider doesn't name the loci in its list, so I used the
script from The Simple Fool's Guide to Population Genomics via RNA-Seq available at

There are instructions for the script at the following webpage: you just need to scroll down to "3)FST Outliers" to find the instructions once you are on the page.


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