Minimac Command Reference - Revision history

Cfuchsb at 07:40, 28 January 2015

2015-01-28T07:40:36Z

← Older revision		Revision as of 03:40, 28 January 2015
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	; --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 ==

Cfuchsb at 07:21, 11 September 2014

2014-09-11T07:21:59Z

← Older revision		Revision as of 03:21, 11 September 2014
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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 ==

Cfuchsb at 17:25, 18 October 2013

2013-10-18T17:25:15Z

← Older revision		Revision as of 13:25, 18 October 2013
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	== Target Haplotype Set ==		== Target Haplotype Set ==

			=== MaCH Format ===

	; --snps [filename]		; --snps [filename]
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	; --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 ==

Cfuchsb: /* Reference Haplotype Set */

2012-10-03T20:02:33Z

Reference Haplotype Set

@@ Line 12: / Line 12: @@
 ;  --vcfReference
 : This option specifies that the provided --refHaps file is provided in [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] , no --refSNPs file needed.
 ; --snpAliases [filename]

Cfuchsb: /* Target Haplotype Set */

2012-07-25T01:00:46Z

Target Haplotype Set

← Older revision		Revision as of 21:00, 24 July 2012
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	; --haps [filename]		; --haps [filename]
	: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]]. The file should be formatted just like the reference haplotype file, described in the previous section.		: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]]. The file should be formatted just like the reference haplotype file, described in the previous section.

			; --rs
			: In combination with --vcfReference, allows to use rs GWAS SNP identifiers

	== Model Refinement ==		== Model Refinement ==

Cfuchsb: /* Reference Haplotype Set */

2012-07-25T01:00:38Z

Reference Haplotype Set

← Older revision		Revision as of 21:00, 24 July 2012
Line 15:		Line 15:
	; --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://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].

	~~; --rs~~
	~~: In combination with --vcfReference, allows to use rs GWAS SNP identifiers~~

	== Target Haplotype Set ==		== Target Haplotype Set ==

Cfuchsb: /* Reference Haplotype Set */

2012-07-25T01:00:11Z

Reference Haplotype Set

← Older revision		Revision as of 21:00, 24 July 2012
Line 15:		Line 15:
	; --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://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].

			; --rs
			: In combination with --vcfReference, allows to use rs GWAS SNP identifiers

	== Target Haplotype Set ==		== Target Haplotype Set ==

Cfuchsb: /* Reference Haplotype Set */

2012-04-19T23:31:16Z

Reference Haplotype Set

← Older revision		Revision as of 19:31, 19 April 2012
Line 10:		Line 10:
	: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T","I","D","R" (I..Insertions, D..Deletion, R..Reference); upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".		: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T","I","D","R" (I..Insertions, D..Deletion, R..Reference); upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".

	; --~~vcf~~		; --vcfReference
	: This option specifies that the provided --refHaps file is provided in [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] , no --refSNPs file needed.		: This option specifies that the provided --refHaps file is provided in [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] , no --refSNPs file needed.

Cfuchsb: /* Reference Haplotype Set */

2012-03-01T22:48:45Z

Reference Haplotype Set

← Older revision		Revision as of 18:48, 1 March 2012
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	; --vcf		; --vcf
	: This option specifies that the provided --refHaps file is ~~saved~~ in ~~the~~ [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] - no --refSNPs file needed.		: This option specifies that the provided --refHaps file is provided in [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] , no --refSNPs file needed.


	; --snpAliases [filename]		; --snpAliases [filename]

Cfuchsb: /* Reference Haplotype Set */

2012-03-01T22:45:01Z

Reference Haplotype Set

← Older revision		Revision as of 18:45, 1 March 2012
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	; --refHaps [filename]		; --refHaps [filename]
	: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]].		: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]].
	: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T"; upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".		: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T","I","D","R" (I..Insertions, D..Deletion, R..Reference); upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".

			; --vcf
			: This option specifies that the provided --refHaps file is saved in the [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] - no --refSNPs file needed.


	; --snpAliases [filename]		; --snpAliases [filename]