snipar.scripts.gts_matrix module
Output multidimensional array with proband and (imputed/observed) parental genotypes
- Args:
- ‘-h’, ‘–help’, default===SUPPRESS==
show this help message and exit
- ‘–bgen’str
Address of the phased genotypes in .bgen format. If there is a @ in the address, @ is replaced by the chromosome numbers in the range of chr_range for each chromosome (chr_range is an optional parameters for this script).
- ‘–bed’str
Address of the unphased genotypes in .bed format. If there is a @ in the address, @ is replaced by the chromosome numbers in the range of chr_range for each chromosome (chr_range is an optional parameters for this script).
- ‘–imp’str
Address of hdf5 files with imputed parental genotypes (without .hdf5 suffix). If there is a @ in the address, @ is replaced by the chromosome numbers in the range of chr_range (chr_range is an optional parameters for this script).
- ‘–chr_range’
number of the chromosomes to be imputed. Should be a series of ranges with x-y format or integers.
- ‘–out’str, default=./
The summary statistics will output to this path, one file for each chromosome. If the path contains ‘@’, the ‘@’ will be replaced with the chromosome number. Otherwise, the summary statistics will be output to the given path with file names chr_1.sumstats.gz, chr_2.sumstats.gz, etc. for the text sumstats, and chr_1.sumstats.hdf5, etc. for the HDF5 sumstats
- ‘–pedigree’str
Address of pedigree file. Must be provided if not providing imputed parental genotypes.
- ‘–parsum’
Regress onto proband and sum of (imputed/observed) maternal and paternal genotypes. Default uses separate paternal and maternal genotypes when available.
- ‘–fit_sib’
Fit indirect effect from sibling
- ‘–min_maf’float, default=0.01
Ignore SNPs with minor allele frequency below min_maf (default 0.01)
- ‘–threads’int
Number of threads to use for IBD inference. Uses all available by default.
- ‘–max_missing’float, default=5
Ignore SNPs with greater percent missing calls than max_missing (default 5)
- Results:
- gts_matrix.hdf5
For each chromosome, a HDF5 file containing proband and (imputed/observed) parental genotypes
- snipar.scripts.gts_matrix.gts_matrix_chromosome(chrom_out, pedigree, outprefix, bedfile=None, bgenfile=None, par_gts_f=None, fit_sib=False, parsum=False, max_missing=5, min_maf=0.01)[source]
- snipar.scripts.gts_matrix.main(args)[source]
“Calling this function with args is equivalent to running this script from commandline with the same arguments. Args:
- args: list
list of all the desired options and arguments. The possible values are all the values you can pass this script from commandline.