User: Avsmith

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Avsmith280
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Reykjavik, Iceland
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Posts by Avsmith

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Comment: C: How To Analyze Imputed Gwas Data
... I should add that I am intrigued by compression options in ncdf4, as these files are HUGE. However, I've never ported over to ncdf4. ...
written 8.7 years ago by Avsmith280
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Answer: A: How To Analyze Imputed Gwas Data
... As I mentioned in my previous answer, the packages mentioned above are good at set models, but can't alway do exactly the analysis you'd like to do. When doing that, I typically work via netcdf stored versions of the genotypes. I don't work this way unless necessary, as it is **MUCH**, **MUCH** slo ...
written 8.7 years ago by Avsmith280 • updated 12 weeks ago by RamRS25k
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Comment: C: How To Analyze Imputed Gwas Data
... Since I wrote this last night, all the GenABEL & ProbABEL links appear to have changed. Will re-edit after the links are all fixed at the new site. ...
written 8.7 years ago by Avsmith280
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Answer: A: How To Analyze Imputed Gwas Data
... For imputation, the primary QC really should be done on the input genotypes, rather than directly on the imputations. Prior to imputation, I remove SNPs at MAF < 0.01, HWE < 1e-06, and only used SNPs present on 97% of the samples. Also, since Illumina data has relatively few A/T and G/C SNPs, ...
written 8.7 years ago by Avsmith280

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