Output Genotype file format used in PCA analyses

jha...@nevada.unr.edu

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Apr 25, 2016, 5:18:51 PM4/25/16

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Hi All,

I have been searching the Stacks tutorials and I am unable to find information on how to export genotype files in a format used in principal components analyses. Is stacks able to do this? I have sequenced what is believed to be 3 populations and want to run a few PCAs on the data. I tried genotypes function but it doesn't give out the formatted needed for these analyses.

ind1_id genotype_locus1 genotype_locus2 genotype_locus3 genotype_locus4 genotype_locus5 ...
ind2_id genotype_locus1 genotype_locus2 genotype_locus3 genotype_locus4 genotype_locus5 ...
ind3_id genotype_locus1 genotype_locus2 genotype_locus3 genotype_locus4 genotype_locus5 ...
ind4_id genotype_locus1 genotype_locus2 genotype_locus3 genotype_locus4 genotype_locus5 ...

where the first column is the ID and subsequent columns are the loci. 0=homozygous 1=heterzygous 2=homozygous

Any help would be greatly appreciated.

-Josh Hallas

Louis Plough

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Apr 25, 2016, 10:37:21 PM4/25/16

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I would read the manual/info on the 'populations' module . You can export to any number of standard pop gen genotype formats. e.g. Genepop is a good one for downstream analyses like PCA.

LP

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Claire Daguin Thiébaut

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Apr 26, 2016, 2:43:14 AM4/26/16

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Hi all,

you can also use the vcf file output from "populations". Then you can use the StackR package (https://github.com/thierrygosselin/stackr) to transform your vcf into a genind file with the vcf2genind function. The genind file will be use as an input for producing the PCA with Adegenet.

Cheers

Claire Daguin Thiebaut

Joshua Hallas

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Apr 26, 2016, 10:46:02 AM4/26/16

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Thanks for the help Claire.

-josh

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Joshua M. Hallas

PhD. Student, Parchman Lab

Ecology, Evolution, and Conservation Biology

University of Nevada, Reno

1664 N. Virginia St.
Reno, Nevada 89557
https://jmhallasresearch.wordpress.com/
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