User: whit18

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whit1820
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1 year, 8 months ago
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Posts by whit18

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Strand Alignment in ShapeIt -- "Reference and Main panels are not well aligned"
... 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 ...
shapeit gwas alignment written 23 months ago by whit1820 • updated 7 weeks ago by Kevin Blighe52k
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Comment: C: From Impute2 to PLINK: when to merge chromosome files?
... Great, thanks! I can't find any good alternatives, but I'll definitely try merge-list ...
written 23 months ago by whit1820
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From Impute2 to PLINK: when to merge chromosome files?
... 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!! ...
impute2 imputation plink gwas written 23 months ago by whit1820 • updated 23 months ago by Wietje220
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Comment: C: Help Please! Stuck in .bed format and need to convert for Impute2
... "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 2.0 years ago by whit1820
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Help Please! Stuck in .bed format and need to convert for Impute2
... 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 ...
impute2 liftover written 2.1 years ago by whit1820

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