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fastlmm / FaST-LMM

Python version of Factored Spectrally Transformed Linear Mixed Models
https://fastlmm.github.io/
Apache License 2.0
47 stars 11 forks source link

Hapmap format #28

Closed snowformatics closed 2 years ago

snowformatics commented 2 years ago

Hi everyone,

Does anyone has experience with genotypic data stored in Hapmap format? What would be the best approach to convert the data? Would it work to convert it to hdf5 or must I go for Hapmap > vcf > bed?

Thanks for any tips

CarlKCarlK commented 2 years ago

Hi,

I think FaST-LMM's flavor of HDF5 is different than anyone else's, so Hapmap, to VCF, to PLINK Bed is likely necessary.

I did see this for converting from hapmap to PLINK Bed format: http://poissonfish.github.io/iPat/convert-hapmap-to-plink-format.html

And as you likely already know the plink tool is good for VCF to PLINK Bed https://www.researchgate.net/post/Coverting-vcf-files-to-plink-bed-format

From: snowformatics @.> Sent: Monday, March 14, 2022 12:17 AM To: fastlmm/FaST-LMM @.> Cc: Subscribed @.***> Subject: [fastlmm/FaST-LMM] Hapmap format (Issue #28) Importance: High

Hi everyone,

Does anyone has experience with genotypic data stored in Hapmap format? What would be the best approach to convert the data? Would it work to convert it to hdf5 or must I go for Hapmap > vcf > bed?

Thanks for any tips

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snowformatics commented 2 years ago

Thanks Carl, I used Tassel to convert the file and it worked very well!