I'm 100% new to Bioinformatics and terrible with computers (medical doctor). 'Currently working on a GWAS with the data from the Human Connectome Project (HCP). Running into some issues, please bear with me if my description of the issue isn*t optimal
Already have the Phenotypes from the HCP webpage in .csv format
This is how my .fam file looks like
52259_82122 100004 52259 82122 1 -9 56037_85858 100206 56037 85858 1 -9 51488_81352 100307 51488 81352 2 -9 51730_81594 100408 51730 81594 1 -9 52813_82634 100610 52813 82634 1 -9 51283_52850_81149 101006 51283 81149 2 -9 51969_81833 101107 51969 81833 1 -9 51330_81195 101208 51330 81195 2 -9 52385_82248 101309 52385 82248 1 -9 52198_82061 101410 52198 82061 1 -9
This is how my phenotype .cvs file looks like
So from what I know until now, I have to attach a phenotype to the .fam file. So I try the following. Using age as an example phenotype
./plink --bfile genotypefile --pheno phenotype.csv --pheno-name Age_in_Yrs --make-bed --out filename
and this happens:
aldo@dell1:~/Desktop/PLINK$ ./plink --bfile MEGA_Chip --pheno rest.csv --pheno-name Age_In_Years --make-bed --out mergedage PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to mergedage.log. Options in effect: --bfile MEGA_Chip --make-bed --out mergedage --pheno rest.csv --pheno-name Age_In_Years 32117 MB RAM detected; reserving 16058 MB for main workspace. 2119803 variants loaded from .bim file. 1141 people (523 males, 618 females) loaded from .fam. Error: Line 1 of --pheno file has fewer tokens than expected.
So i'm stuck at this error (Line 1 of --pheno file has fewer tokens than expected.). Modifying the phenotype.csv is a non issue, the file is small. However, I can't open the .ped file because it too big (9.7GB) and my computer just dies trying to do so.
Somehow yesterday I managed to modify the phenotype.csv in a way that the error turned into Line 1 of --(.ped , i think) file has fewer tokens than expected. I seem to have deleted columns or shifted them so that they matched (FID IID).
Any help would be appreciated