Question: STRUCTURE software file format
2
gravatar for bruseq
3.3 years ago by
bruseq40
bruseq40 wrote:

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 :-)

ADD COMMENTlink modified 18 months ago by Giovanni.madrigal12170 • written 3.3 years ago by bruseq40
3
gravatar for Giovanni.madrigal12
18 months ago by
Giovanni.madrigal12170 wrote:

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

ADD COMMENTlink written 18 months ago by Giovanni.madrigal12170
2
gravatar for rimgubaev
18 months ago by
rimgubaev180
Russia/Moscow/Skoltech
rimgubaev180 wrote:

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

ADD COMMENTlink written 18 months ago by rimgubaev180
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