Minimac: GIANT 1000 Genomes Imputation Cookbook - Revision history

Cfuchsb: Redirected page to Minimac: 1000 Genomes Imputation Cookbook

2012-07-25T03:06:51Z

Redirected page to Minimac: 1000 Genomes Imputation Cookbook

← Older revision		Revision as of 23:06, 24 July 2012
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	#~~AutoRedirect~~[[Minimac:_1000_Genomes_Imputation_Cookbook]]		#REDIRECT[[Minimac:_1000_Genomes_Imputation_Cookbook]]

Cfuchsb at 03:06, 25 July 2012

2012-07-25T03:06:38Z

← Older revision		Revision as of 23:06, 24 July 2012
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	#~~REDIRECT~~[[Minimac:_1000_Genomes_Imputation_Cookbook]]		#AutoRedirect[[Minimac:_1000_Genomes_Imputation_Cookbook]]

Cfuchsb: Redirected page to Minimac: 1000 Genomes Imputation Cookbook

2012-07-25T03:05:36Z

Redirected page to Minimac: 1000 Genomes Imputation Cookbook

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Cfuchsb: /* Imputation into Phased Haplotypes - minimac */

2012-07-25T00:59:02Z

Imputation into Phased Haplotypes - minimac

← Older revision		Revision as of 20:59, 24 July 2012
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	A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:		A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:

	minimac --refHaps ref.~~hap.$chr~~.gz ~~--vcfReference~~ --haps ~~chr$chr~~.~~haps~~.gz --snps ~~chr~~.~~$chr~~.~~snps~~ --prefix chr~~$chr~~.~~imputed~~		== using a VCF reference panel ==
			minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
			Note: GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19;
			otherwise, please set the --rs flag


	A detailed description of all minimac options is available [[Minimac Command Reference\|elsewhere]]. Here is a brief description of the above parameters:		A detailed description of all minimac options is available [[Minimac Command Reference\|elsewhere]]. Here is a brief description of the above parameters:

Cfuchsb: /* Reference Haplotypes */

2012-07-25T00:57:23Z

Reference Haplotypes

← Older revision		Revision as of 20:57, 24 July 2012
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	=== Reference Haplotypes ===		=== Reference Haplotypes ===

	Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ MaCH download page]. In our hands, it is ideal to always use the most recent release since generation of additional sequence data, improvements in variant discovery, genotyping and haplotyping strategies typically result in noticeable improvements in data quality. When this page was written, the most recent release of 1000 Genomes project haplotypes was the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G.2012-03-14.html Integrated Phase I release], including ~~1094~~ individuals ~~genotyped at >40 million autosomal~~ sites.		Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ MaCH download page]. In our hands, it is ideal to always use the most recent release since generation of additional sequence data, improvements in variant discovery, genotyping and haplotyping strategies typically result in noticeable improvements in data quality. When this page was written, the most recent release of 1000 Genomes project haplotypes was the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G.2012-03-14.html Integrated Phase I release], including 1092 individuals. We recommend to use the reduced GIANT all population panel (no monomorphic and singleton sites)
			[ftp://share.sph.umich.edu/1000genomes/fullProject/2012.03.14/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz]

	== Minimac Imputation ==		== Minimac Imputation ==

Cfuchsb: /* Further Time Savings */

2012-05-30T13:40:30Z

Further Time Savings

@@ Line 174: / Line 174: @@
 </source>
-A modified script, using [[ChunkChromosome]] would look like this:
+A modified script, using [[ChunkChromosome]] would look like this (chr:pos GWAS SNP IDs):
 <source lang="bash">
@@ Line 206: / Line 206: @@
        minimac --refHaps $haps --refSnps $snps  --vcfReference  \
                --haps ${chunk:r}.gz --snps ${chunk}.snps  --autoClip autoChunk-chr$chr.dat  \
                --prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &

Cfuchsb: /* Your Own Data */

2012-05-30T13:36:04Z

Your Own Data

← Older revision		Revision as of 09:36, 30 May 2012
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	If you are planning to use imputation with the MetaboChip, you might find a list of SNPs whose order varies between NCBI genome build 36 and 37 convenient. Here it is: [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt List of Metabochip SNPs Whose Order Changes With Build]		If you are planning to use imputation with the MetaboChip, you might find a list of SNPs whose order varies between NCBI genome build 36 and 37 convenient. Here it is: [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt List of Metabochip SNPs Whose Order Changes With Build]

	Note: For the most recent reference panel in VCF format by default GWAS SNPs are expected to be in the chr:pos format e.g. 1:1000; otherwise, ~~if you are using rsXXX identifiers~~ you have to set the --rs flag		Note: For the most recent reference panel in VCF format by default GWAS SNPs are expected to be in the chr:pos format e.g. 1:1000; otherwise, for GWAS SNPs in the rs..... format you have to set the --rs flag

	=== Quality Control ===		=== Quality Control ===

Cfuchsb: /* Your Own Data */

2012-05-30T13:35:04Z

Your Own Data

← Older revision		Revision as of 09:35, 30 May 2012
Line 15:		Line 15:
	If you are planning to use imputation with the MetaboChip, you might find a list of SNPs whose order varies between NCBI genome build 36 and 37 convenient. Here it is: [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt List of Metabochip SNPs Whose Order Changes With Build]		If you are planning to use imputation with the MetaboChip, you might find a list of SNPs whose order varies between NCBI genome build 36 and 37 convenient. Here it is: [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt List of Metabochip SNPs Whose Order Changes With Build]

	Note: For the most recent reference panel in VCF format GWAS SNPs ~~have~~ to be in the chr:pos format e.g. 1:1000 ~~(NOT rsxxxxx)~~		Note: For the most recent reference panel in VCF format by default GWAS SNPs are expected to be in the chr:pos format e.g. 1:1000; otherwise, if you are using rsXXX identifiers you have to set the --rs flag

	=== Quality Control ===		=== Quality Control ===

Cfuchsb: /* Imputation into Phased Haplotypes - minimac */

2012-05-29T18:14:34Z

Imputation into Phased Haplotypes - minimac

← Older revision		Revision as of 14:14, 29 May 2012
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	minimac --refHaps ref.hap.$chr.gz --vcfReference --haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed		minimac --refHaps ref.hap.$chr.gz --vcfReference --haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed

	~~chr$chr.haps~~

	A detailed description of all minimac options is available [[Minimac Command Reference\|elsewhere]]. Here is a brief description of the above parameters:		A detailed description of all minimac options is available [[Minimac Command Reference\|elsewhere]]. Here is a brief description of the above parameters:

Cfuchsb: /* Further Time Savings */

2012-05-29T18:06:03Z

Further Time Savings

← Older revision		Revision as of 14:06, 29 May 2012
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	# Impute into phased haplotypes		# Impute into phased haplotypes
	foreach chr (`seq 1 22`)		foreach chr (`seq 1 22`)
	minimac --refHaps ref.hap.$chr.gz --~~refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz~~ \		minimac --refHaps ref.hap.$chr.gz --vcfReference \
	--haps chr$chr.haps.gz --snps chr$chr.snps --prefix chr$chr.imputed >& chr$chr-minimac.log &		--haps chr$chr.haps.gz --snps chr$chr.snps --prefix chr$chr.imputed >& chr$chr-minimac.log &
	end		end