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

Join Date: Nov 2009
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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 (http://cmpg.unibe.ch/software/BayeScan/)..

I tried using file conversion tools such as PGDSpider "http://www.cmpg.unibe.ch/software/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,

regards,

Nandan

Any other tools to do Fst outlier analysis using a "vcf" file with multiple samples?
Attached Files
File Type: ppt Query_PGDSpider_BayeScan.ppt (306.0 KB, 6 views)
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Old 03-23-2017, 11:27 AM   #2
alexbenroland
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Location: cambridge, MA

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Default

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

Best,
Alex
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Old 03-24-2017, 07:34 AM   #3
Gopo
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Location: Louisiana

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Default

PGDSpider doesn't name the loci in its list, so I used the
Code:
make_bayescan_input.py
script from The Simple Fool's Guide to Population Genomics via RNA-Seq available at http://sfg.stanford.edu/Scripts.zip

There are instructions for the script at the following webpage:
http://sfg.stanford.edu/SNP.html you just need to scroll down to "3)FST Outliers" to find the instructions once you are on the page.

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

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