Quantitative Phenotype Scan Statistic (QPSS) is a tool for scan-statistic approach handling continuous outcomes to identify genomic regions where rare quantitative-phenotype-associated variants cluster.
Programming language: Python2
Others: PLINK 1.9, R 2.10 or higher, R packages goft
Options:
--bfile = input PLINK binary fileset (i.e., .bed/bim/fam) (required)
--chr = chromosome number (required)
--G-position = start and end positions of G (default: start and end positions in PLINK bfile)
--pheno = phenotype file with FID (first column), IID (second column)
--pheno-name = column name for phenotype in phenotype file
--max-maf - max threshold of MAF to define rare variant (default: 0.05)
--min-ac = min threshold of MAC to define rare variant (default: 5)
--extract = list to extract variants
--exclude = list to exclude variants
--keep = list to keep individuals
--remove = list to remove individuals
--W-position or --W = start and end positions of W
--W-file = list of start and end positions
--W-fixed or --wf = window size for sliding window approach (default: 2000)
--W-slide or --ws = slid window size for sliding window approach (default: half of window size specified by --W-fixed)
--out" = output file name
--perm or --p = whether p is computed. Add 'gpd' as --perm gpd for GPD approximation
--threads = number of threads used (default: 10)
--max-sim = max number of simulation for permutation test (default: 10000)\
Example 1: sliding window approach (W = 2000/S = 1000) for entire chromosome 1 for outcome in a phenotype file to output logLR only
$ python2 QPSS.v1.py --bfile plink_fileset_name --pheno phenotype_file_name --pheno-name outcome_name --chr 1 --out output_name
Example 2: calculate logLR and p-value by permutation test for a specfic window (start = 1234 and end = 5678) on chromosome 1
$ python2 QPSS.v1.py --bfile plink_fileset_name --pheno phenotype_file_name --pheno-name outcome_name --chr 1 --W-position 1234 5678
Example 3: calculate logLR and p-value with GPD approximation for a specfic window (start is 1234 and end is 5678) within a specfic G region (start 123 to end 456789) on chromosome 1 --perm
$ python2 QPSS.v1.py --bfile plink_fileset_name --pheno phenotype_file_name --pheno-name outcome_name --chr 1 --W-position 1234 5678 --G-position 123 456789 --perm gpd