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Old 05-16-2016, 11:25 PM   #1
Location: Sydney

Join Date: Nov 2009
Posts: 29
Default GATK multisample vcf to BayeScan input

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?
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File Type: ppt Query_PGDSpider_BayeScan.ppt (306.0 KB, 6 views)
ndeshpan is offline   Reply With Quote
Old 03-23-2017, 11:27 AM   #2
Junior Member
Location: cambridge, MA

Join Date: Dec 2013
Posts: 6

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

alexbenroland is offline   Reply With Quote
Old 03-24-2017, 07:34 AM   #3
Location: Louisiana

Join Date: Nov 2013
Posts: 38

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.

Gopo is offline   Reply With Quote

bayescan, conversion, fst outliers, gatk alignment pipeline, vcf

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