table of contents
| MINIMAC4(1) | General Commands Manual | MINIMAC4(1) |
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¶
Other Parameters¶
SEE ALSO¶
COPYRIGHT¶
Copyright © 2014-2018 Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis
| June 2018 | 1.0.0 |