GWAS qfam-total

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Kirke
Posts: 1
Joined: Tue Feb 10, 2015 7:38 am

GWAS qfam-total

Postby Kirke » Tue Feb 10, 2015 7:46 am

Hi.

I am new to GWAS and are trying to run a qfam-total on my data.
Unfortunately something went wrong, can anybody help me?

this is my script:

Code: Select all

 #!/bin/tcsh

plink-1.9 --bfile /home/projects/AllChr/Sep14/Chr1-22_wPT_raw --keep /home/people/kirke/participantsbetween20and80.txt --make-founders require-2-mising --out qfam_rawfile

plink-1.9 --bfile /home/people/kirke/qfam_rawfile --hwe 0.0001 --maf 0.01 --mind 0.1 --geno 0.05 --make-bed --out qfam_rawfile_qualityc

plink-1.9 --bfile /home/people/kirke/qfam_rawfile_qualityc --indep 50 5 10 --out qfam_rawfile_qualityc_prune

plink-1.9 --extract /home/people/kirke/qfam_rawfile_qualityc_prune.prune.in --bfile /home/people/freja/qfam_rawfile_qualityc --make-bed --out qfam_rawfile_qualityc_prune_extract

plink-1.06 --noweb --silent --bfile /home/people/kirke/qfam_rawfile_qualityc_prune_extract --qfam-total --mperm 1000 --pheno /home/projects/CLN41_NEO_correct_ids_plink.sample --covar /home/projects/covar_sex_age_std.txt --hide-covar --make-bed --out qfam_result

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: GWAS qfam-total

Postby lckarssen » Fri Feb 13, 2015 1:56 pm

Hi Kirke, welcome to our forum. I've decided to move your question from the Journal Club section to the GenABEL section as it is directly related to software tools and not really a discussion of literature.

As to your question: you use Plink for your analyses, but this is the GenABEL forum. Although most of the people on this forum use Plink too it may be handy to have a look at the Plink support page: http://pngu.mgh.harvard.edu/~purcell/pl ... html#probs
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Lennart Karssen
PolyOmica
The Netherlands
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