STRUCTURE software file format
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Entering edit mode
5.0 years ago
bruseq ▴ 40

Hello,

I am optimizing STRUCTURE software for the population genetics analysis. I have a gatk-vcf output file, and tried to convert with plink tool to STRUCTURE file format, but the output is not appropriate, so how to convert vcf file to structure file format. when I load data in STRUCTURE error occurs "Bad data format source" 1 Lines with 1024 columns, 1 Lines with 1023 columns. So please guide me how to format STRUCTURE file format data, and also how to define exact number of column or loci.

Thanks :-)

STRUCTURE SNP POPULATIONGENETICS • 5.7k views
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4
Entering edit mode
3.1 years ago
Gio12 ▴ 200

There is also a python script you can use, located here.

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3
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3.1 years ago
rimgubaev ▴ 280

Try to convert GATK-VCF to structure using PGDSpider. It has a user-friendly interface and it actually works.

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