SHAPEIT 3 USAGE

Basic options:

-H [ –help ] Produce help message.

–seed arg (=1484822686) Seed of the random number generator.

-T [ –thread ] arg (=1) Number of thread used for phasing.

-L [ –output-log ] arg (=shapeit_date_time_UUID.log) Log file containing a duplicate of the screen output.

Subsetting options:

–exclude-snp arg File containing all the positions of the SNPs to exclude in input/output  files.

–include-snp arg File containing all the positions of the SNPs to include in input/output
files.
–exclude-ind arg File containing all the ID of the individuals to exclude in input/output  files.

–include-ind arg File containing all the ID of the individuals to include in input/output
files.

–input-from arg (=0) First physical position to consider in  input files.

–input-to arg (=1000000000) Last physical position to consider in input file.

Input files options:

-B [ –input-bed ] arg Unphased genotypes in Plink BED/BIM/FAM format.

-M [ –input-map ] arg Genetic map in HapMap format.

-G [ –input-gen ] arg Unphased genotypes in Impute2 GEN/SAMPLE format.

–input-thr arg (=0.9) Probability threshold used to call a genotype in GEN file.

-R [ –input-ref ] arg Reference set of haplotypes in HAPS/SAMPLE format.

MCMC options:

–burn arg (=7) Number of burn-in MCMC iterations.

–prune arg (=8) Number of pruning MCMC iterations.

–main arg (=20) Number of main MCMC iterations.

Model options:

-c [ –cluster_burn ] arg (=1) Frequency of clustering in burnin  iterations.

-S [ –states ] arg (=100) Number of hidden states used for  phasing.

–effective-size arg (=15000) Effective size of the population.

–rho arg (=0.0004) Constant recombination rate.

–fast Turn on fast mode. Greater speed with a small decrease in accuracy. (suitable
for N>10,000)

–cluster-size arg cluster size for fast conditioning haplotype search

–early-stopping do not perform HMM calculations when perfect matches are found with conditioning haplotypes

-W [ –window ] arg (=2) Mean size of the windows in which conditioning haplotypes are defined.

Output file options:

-O [ –output-max ] arg Phased haplotypes in Impute2 format.