550
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac Command Reference (view source)
Revision as of 13:25, 18 October 2013
, 13:25, 18 October 2013no edit summary
== 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 ==
