STEROID
INTRODUCTION
STEROID is a tool for calculating genetic risk scores for samples in vcf format files. Genetic risk models should be in LDpred format and these can be calculated for VCF files using imputation probabilities (vcf format fields GP, DS) or called genotypes (GT). Several models can be calculated simoultainously.
DOWNLOAD
INSTALLATION
Copy STEROIDv*.zip file into your computer, unzip the file:
unzip STEROIDv*.zip
To compile STEROID program, use command:
make
in the folder where files have been unpacked. The program can be run by typing:
./STEROID
INPUT FORMATS
Genetic models in LDpred format (https://github.com/bvilhjal/ldpred).
chrom pos sid nt1 nt2 raw_beta ldpred_beta chrom_1 752566 rs3094315 G A 6.0000e-03 -4.2511e-05 chrom_1 768448 rs12562034 A G 2.7000e-03 -1.3897e-05 chrom_1 779322 rs4040617 G A 6.2000e-03 -4.6578e-05 chrom_1 785989 rs2980300 T C 5.5000e-03 -3.4656e-05
Samples should in standard VCF v4.2 format for chromosome in the first column without "chr" in front of number.
RUNNING STEROID
Reading command line options:
USAGE:
./STEROID [--field <string>] -o <string> [--chr <int>] --vcf <string>
--gwas <string> ... [--] [--version] [-h]
Where:
--field <string>
This specifies VCF format field to use. Default is GP (options: GP, DS
, GT)
-o <string>, --out <string>
(required) This specifies output file
--chr <int>
This specifies vcf file chromosome. Dont use this option if vcf
contains several chromosomes
--vcf <string>
(required) This specifies VCF file
--gwas <string> (accepted multiple times)
(required) Name of LDpred output file (in case of several files, use
this command multiple times
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
EXAMPLE COMMAND LINE:
./STEROID --vcf DATA_chr22.vcf.gz --gwas xxx_LDpred-inf --gwas xxx_LDpred_p1.0000e+00 --gwas xxx_LDpred_p1.0000e-01 --gwas .xxx_LDpred_p1.0000e-02--out xxx_grs_chr22.txt