Basic Usage
SHAPEIT3 commands are very similar to SHAPEIT2, with a few additional arguments to enable its fast scaling. Simply enabling the --fast flag should be sufficient for most users:
shapeit3 -B example/gwas -M genetic_map.txt -O out --threads 2 --cluster-size 500
A full list of arguments are listed below. In addition to the standard SHAPEIT2 parameters, SHAPEIT3 has the following arguments:
| Option | Description |
|---|---|
| –fast | Turn on fast mode. Greater speed with a small decrease in |
| –cluster-size arg | cluster size for fast conditioning haplotype search. We have found 4000 provides a good tradeoff |
| –early-stopping | do not perform HMM calculations when perfect matches are found with conditioning haplotypes |
Full list of options
Basic options:
| Option | Description |
|---|---|
| -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:
| Option | Description |
|---|---|
| –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:
| Option | Description |
|---|---|
| -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:
| Option | Description |
|---|---|
| –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:
| Option | Description |
|---|---|
| -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. Accuracy and computation time will increase with this value. We have found 4000 provides a good tradeoff | |
| –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:
| Option | Description |
|---|---|
| -O [ –output-max ] arg | Phased haplotypes in Impute2 format. |