genotype match with phenotype

[lorenasala]

Hello, I am new to this analysis, I would like to know how you can match your patient's genotype with its phenotype, can you please load up the code?

Thanks so much

[SynaSpike]

The genotypes ID must be the same or at least a subset of the phenotypes ID. For instance, if you have a phenotype ID as following TGF-123F-SM-1230 (after the SM part standing for the aliquot), having your genotype ID as TGF-123F would work.
However it's rarely the case since genotype data and phenotype data seem to stem from different aliquots and that their full ID patterns are used in your dataframes.

if you look at the GTEx pipeline (https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl), there is a preparation step where you can build a tsv file to set a correspondance between your phenotype and genotype IDs. However, it did not work form me. So what I've done is: when the bed file preparation is completed, I just renamed the dataframe column names with a dictionnary with the genotype IDs (with a 1-1 correspondance) then your bed file column names correspond to the genotype IDs in your vcf.

Hope this can help!