faststructure and vcf tools

[Karine Durand]

Hello
i try to make an imput file for faststructure. I have a vcf file but my SNP are in row and i have 272 000 SNPs. So how can i make a vcf file with my samples in row and SNPs in colunns? if i try to do it manually it's impossible because excel can't open 272000 colunns and i can't use vcftools --vcf mydata --plink to create a .fam, .bim and .bed files for faststructure.
Can you help me?
thanks

[Vikram Chhatre]

Hi Karine,

You can use PGDspider to convert from VCF to fastStructure.  You will need a lot of memory for doing this.  So if you have access to a cluster, do this there.  Use as much memory as you have access to.

V

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[Karine Durand]

Thanks a lot it's nice, but i have another question How can you create the .bam and .bim files with your PGDspider file?

[Vikram Chhatre]

You can't with PGD, but you don't need to.  FastStructure can use either of the two formats:

- Structure

- Plink Bed

With PGD, you can convert VCF to Structure (make sure you use the fastStr option in the settings file).

V

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