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GWAS qfam-total

Posted: Tue Feb 10, 2015 7:46 am
by Kirke
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

Re: GWAS qfam-total

Posted: Fri Feb 13, 2015 1:56 pm
by lckarssen
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