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DReichLab / EIG

Eigen tools by Nick Patterson and Alkes Price lab
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(getpedgenos) bad geno <DEL> #74

Open Zymaniswenzai opened 2 years ago

Zymaniswenzai commented 2 years ago

Hi, smartpca team. Thanks for developing such great software!

I imputed my .vcf file and converted them to .ped file for smartpca analysis. But there is an error: image I checked my .ped file and it did have <DEL> in it.

21638495908_ pic_hd

I don't know why the <DEL> appears and want to know what should I do to get my analysis going.

Thanks for any help!

JW

bumblenick commented 2 years ago

My software doesn't support strings like GAACA as a single "genotype"

Nick

On Tue, Jan 4, 2022 at 3:09 AM Jingwen Gong @.***> wrote:

Hi, smartpca team. Thanks for developing such great software!

I imputed my .vcf file and converted them to .ped file for smartpca analysis. But there is an error: [image: image] https://user-images.githubusercontent.com/30076901/148027964-b4a714ce-766c-4c17-b89e-5fbf35d91ae9.png I checked my .ped file and it did have in it.

[image: 21638495908_ pic_hd] https://user-images.githubusercontent.com/30076901/148028028-92f0281d-1ad1-4b87-9165-6c280f86f965.jpg

I don't know why the appears and want to know what should I do to get my analysis going on.

Thanks for any help!

JW

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