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Revision as of 03:40, 28 January 2015
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[[Minimac]] runs are controled by a series of command line parameters that specify input file names, an initial model for recombination and error rates, an optional series of iterations of model refinement using either [[Monte-Carlo]] methods or an [[Expectation-Maximization]] algorithm, and output file names.
[[Minimac]] and [[Minimac2]] runs are controled by a series of command line parameters that specify input file names, an initial model for recombination and error rates, an optional series of iterations of model refinement using either [[Monte-Carlo]] methods or an [[Expectation-Maximization]] algorithm, and output file names.
== Reference Haplotype Set ==
== Reference Haplotype Set ==
; --snpAliases [filename]
; --snpAliases [filename]
: This option points to a file listing mappings between alternate marker names. Each row should include two columns. The first column lists a previous commonly used name for a marker (perhaps from an earlier version of dbSNP) and the second column lists the current preferred name for the marker. An example input file, which maps ids from the 1000 Genomes Project and earlier versions of dbSNP to dbSNP build 134, see [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].
: This option points to a file listing mappings between alternate marker names. Each row should include two columns. The first column lists a previous commonly used name for a marker (perhaps from an earlier version of dbSNP) and the second column lists the current preferred name for the marker. An example input file, which maps ids from the 1000 Genomes Project and earlier versions of dbSNP to dbSNP build 134, see [http://csg.sph.umich.edu/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].
== Target Haplotype Set ==
== Target Haplotype Set ==
=== MaCH Format ===
; --snps [filename]
; --snps [filename]
; --rs
; --rs
: In combination with --vcfReference, allows to use rs GWAS SNP identifiers
: In combination with --vcfReference, allows to use rs GWAS SNP identifiers
=== ShapeIT Format ===
; --sample [filename]
: Sample list in ShapeIT format
;--shape_haps [filename]
: ShapeIT phased haplotypes where missing genotypes will be imputed.
;--chr [integer]
: Chromosome for which we will carry out imputation (needed to run ShapeIT with chr:pos identifiers - default setting).
== Model Refinement ==
== Model Refinement ==
