Awesome
PRSice-nf
Pipeline to compute polygenic risk scores
Input
Type --help to get the full list of options. All parameters are prefixed with a double-dash like in --help.
| Name | Example value | Description |
|---|---|---|
bgen_list | bgen_list.txt | Txt file containing the list of bgen files to consider (one file per chromosome) |
base_file | base.txt | file containing association analysis results for SNPs on the base phenotype |
pheno_file | pheno.txt | phenotype file: the first two column of the phenotype file should be the FID and the IID and the rest of the columns the phenotypes |
For more details on the files content, see PRSice2 documentation
Parameters
-
Mandatory
| Name | Example value | Description |
|---|---|---|
bgenix | bgenix | path to bgenix executable |
PRSice_path | path_PRSice | path to PRSice scripts |
-
Optional
| Name | Example value | Description |
|---|---|---|
a1_col | 4 | Column number associated with the effect allele (Default value is 4) |
a2_col | 5 | Column number associated with the reference allele (Default value is 5) |
qual_val | 0.3 | Quality threshold. Any SNPs with a value bellow this threshold will be excluded. (Default value is 0) |
pval_thr | 0.0001,0.1,1 | pvalue threshold to consider to select SNPs to include in the PRS |
To install:
Nextflow command line
nextflow run IARCbioinfo/PRSice-nf \
--base_file base.txt \
--pheno_file /data/gep/MR_Signatures/work/gabriela/GIT_Rstudio_project/results/PRSice_res/TCGA_samples.txt --pval_thr 1 \
--output_name ${trait} --output_folder /data/gcs/prs-computation/work/gabriela/PRS_R_project/results/PRSice_res/${trait}/ \
--bgenix path_to_bgenix --PRSice_path path_to_PRSice \
--bgen_list bgen_list.txt \
--bgen_snps_perCHR /data/gep/MR_Signatures/work/gabriela/GIT_Rstudio_project/results/PRSice_res/TCGA_bgen_SNPs/ --qual_val 0.3