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