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