NAME¶
minimac4 - Fast Imputation Based on State Space Reduction HMM
DESCRIPTION¶
Minimac4 is a lower memory and more computationally efficient implementation of
"minimac2/3".
It is an algorithm for genotypic imputation that works on phased
genotypes (say from MaCH). Minimac4 is designed to handle very large
reference panels in a more computationally efficient way with no loss of
accuracy. This algorithm analyzes only the unique sets of haplotypes in
small genomic segments, thereby saving on time-complexity, computational
memory but no loss in degree of accuracy.
OPTIONS¶
Reference Haplotypes¶
- --refHaps
- M3VCF file containing haplotype data for reference panel.
- --passOnly
- This option only imports variants with FILTER = PASS.
- --rsid
- This option only imports RS ID of variants from ID column (if
available).
GWAS Haplotypes¶
- --haps
- File containing haplotype data for target (gwas) samples. Must be VCF
file. Zipped versions allowed.
Output Parameters¶
- --prefix
- Prefix for all output files generated. By default: [Minimac4.Output]
- --processReference
- This option will only convert an input VCF file to M3VCF format (currently
de-activated in minimac4). If this option is ON, no imputation would be
performed.
- --nobgzip
- If ON, output files will NOT be gzipped.
- --format
- Specifies which fields to output for the FORMAT field in output VCF file.
Available handles: GT,DS,HDS,GP [Default: GT,DS].
- --allTypedSites
- If ON, sites available ONLY in GWAS panel will also be output [Default:
OFF].
Subset Parameters¶
- --chr
- Chromosome number for which to carry out imputation.
- --start
- Start position for imputation by chunking.
- --end
- End position for imputation by chunking.
- --window
- Length of buffer region on either side of --start and
--end.
Other Parameters¶
- --log
- If ON, log will be written to $prefix.logfile.
- --help
- If ON, detailed help on options and usage.
- --cpus
- Number of cpus for parallel computing. Works only with Minimac4-omp.
COPYRIGHT¶
Copyright © 2014-2018 Sayantan Das, Christian Fuchsberger, David Hinds
Mary Kate Wing, Goncalo Abecasis
