User: whit18
whit18 • 20
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Posts by whit18
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... I followed the code on ShapeIt's website (http://www.shapeit.fr/pages/m03_phasing/imputation.html) to check strand alignment, and the results don't make sense, with the vast majority of the SNPs being listed as missing in the reference panel. The output is below in case it's helpful. I confirmed the ...
written 2.9 years ago by
whit18 • 20
• updated
13 months ago by
Kevin Blighe ♦ 67k
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... Great, thanks! I can't find any good alternatives, but I'll definitely try merge-list ...
written 2.9 years ago by
whit18 • 20
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... After Impute2, I'll have one file for each chromosome. I saw that PLINK can take each file, convert form binary, and then in another step merge them. Is this the best way to merge the chromosome files? Or is it better to merge the files before PLINK?
Thanks!! ...
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... "The first 5 entries of each line should be the SNP ID, RS ID of the SNP, base-pair position of the SNP, the allele coded A and the allele coded B."
http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html ...
written 3.0 years ago by
whit18 • 20
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... I started with PLINK data files, and changed the .map file over to the UCSC .bed format in order to do LiftOver. Now I have the output from that (in UCSC .bed format), and need to get it ready for Impute2, but cannot figure how to change it into Impute2's required input format.
At this point, I'd ...
written 3.0 years ago by
whit18 • 20
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