ChunkChromosome - Revision history

Ppwhite: /* Download */

2017-02-02T14:02:51Z

Download

← Older revision		Revision as of 10:02, 2 February 2017
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	== Download ==		== Download ==

	You can download source code for the ChunkChromosome program in a tar-ball archive [http://~~www~~.sph.umich.edu/~~csg~~/cfuchsb/generic-ChunkChromosome-2014-05-27.tar.gz generic-ChunkChromosome-2014-05-27.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.		You can download source code for the ChunkChromosome program in a tar-ball archive [http://csg.sph.umich.edu//cfuchsb/generic-ChunkChromosome-2014-05-27.tar.gz generic-ChunkChromosome-2014-05-27.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.

Goncalo at 21:59, 4 September 2014

2014-09-04T21:59:31Z

← Older revision		Revision as of 17:59, 4 September 2014
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	''ChunkChromosome'' is a helper utility for [[minimac]] and [[MaCH]]. It can be used to facilitate analyses of very large datasets in overlapping slices.		''ChunkChromosome'' is a helper utility for [[minimac]] and [[MaCH]]. It can be used to facilitate analyses of very large datasets in overlapping slices. For information on how to put the resulting chunks back together, see [[Ligate Minimac\|this page]].

	== Parameters ==		== Parameters ==

Cfuchsb at 13:56, 27 May 2014

2014-05-27T13:56:09Z

← Older revision		Revision as of 09:56, 27 May 2014
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	== Download ==		== Download ==

	You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/cfuchsb/generic-ChunkChromosome-~~2012~~-08-28.tar.gz generic-ChunkChromosome-~~2012~~-08-28.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.		You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/cfuchsb/generic-ChunkChromosome-2014-05-27.tar.gz generic-ChunkChromosome-2014-05-27.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.

Cfuchsb: /* Download */

2012-08-28T20:22:26Z

Download

← Older revision		Revision as of 16:22, 28 August 2012
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	== Download ==		== Download ==

	You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/~~abecasis/downloads~~/generic-ChunkChromosome-~~2011~~-08-05.tar.gz generic-ChunkChromosome-~~2011~~-08-05.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.		You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/cfuchsb/generic-ChunkChromosome-2012-08-28.tar.gz generic-ChunkChromosome-2012-08-28.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.

Cfuchsb at 02:39, 11 August 2011

2011-08-11T02:39:30Z

← Older revision		Revision as of 22:39, 10 August 2011
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	<source lang="bash">		<source lang="bash">
	ChunkChromosome -d ~~chr1~~.dat		#!/bin/tcsh

			@ length = 2500
			@ overlap = 500

			# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
			foreach chr (`seq 1 22`)

			ChunkChromosome -d chr$chr.dat -n $length -o $overlap

			foreach chunk (chunk*-chr$chr.dat)

			mach -d $chunk -p chr$chr.ped --prefix ${chunk:r} \
			--rounds 20 --states 200 --phase --sample 5 >& ${chunk:r}-mach.log &

			end

	~~# Phase each chunk in parallel~~
	~~foreach chunk (chunk*-chr1.dat)~~
	~~mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r} >& ${chunk:r}-mach.log &~~
	end		end
	wait		wait

	# Impute ~~each chunk in parallel~~		# Impute into phased haplotypes
	foreach chunk (chunk*-~~chr1~~.dat)		foreach chr (`seq 1 22`)
	~~minimac --autoClip autoChunk-chr1~~.~~dat \~~
	--refHaps ~~1000genomes.chr1.~~haps~~.gz~~ --refSnps ~~1000genomes.chr1.~~snps --rounds 5 --states 200 \		foreach chunk (chunk*-chr$chr.dat)
	--haps ${chunk:r}.gz --snps ${chunk}.snps --prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
			set haps = /data/1000g/hap/all/20101123.chr$chr.hap.gz
			set snps = /data/1000g/snps/chr$chr.snps

			minimac --refHaps $haps --refSnps $snps --rounds 5 --states 200 \
			--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
			--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &

			end

	end		end
	wait		wait

Goncalo: /* Usage */

2011-08-05T14:05:21Z

Usage

← Older revision		Revision as of 10:05, 5 August 2011
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	awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps		awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps
	mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps		mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps
	minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix ~~imputation-results~~		minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix chr1.imputed
	</source>		</source>

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	# Phase each chunk in parallel		# Phase each chunk in parallel
	foreach chunk (chunk*-chr1.dat)		foreach chunk (chunk*-chr1.dat)
	mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r}~~.haps~~ >& ${chunk:r}-mach.log &		mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r} >& ${chunk:r}-mach.log &
	end		end
	wait		wait
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	minimac --autoClip autoChunk-chr1.dat \		minimac --autoClip autoChunk-chr1.dat \
	--refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --rounds 5 --states 200 \		--refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --rounds 5 --states 200 \
	--haps ${chunk:r}~~.haps~~.gz --snps ${chunk}.snps --prefix ${chunk:r}~~-results~~ >& ${chunk:r}-minimac.log &		--haps ${chunk:r}.gz --snps ${chunk}.snps --prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
	end		end
	wait		wait

Goncalo: /* Download */

2011-08-05T12:55:22Z

Download

← Older revision		Revision as of 08:55, 5 August 2011
Line 43:		Line 43:
	== Download ==		== Download ==

	You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/abecasis/downloads/generic-ChunkChromosome-2011-08-05.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.		You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/abecasis/downloads/generic-ChunkChromosome-2011-08-05.tar.gz generic-ChunkChromosome-2011-08-05.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.

Goncalo: /* Download */

2011-08-05T12:55:02Z

Download

← Older revision		Revision as of 08:55, 5 August 2011
Line 43:		Line 43:
	== Download ==		== Download ==

	You can download source code for the ChunkChromosome program ~~from~~ [~~here~~]. After downloading it, unpack the archive and use Make to compile the tool.		You can download source code for the ChunkChromosome program in a tar-ball archive [http://www.sph.umich.edu/csg/abecasis/downloads/generic-ChunkChromosome-2011-08-05.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.

Goncalo: /* Download */

2011-08-05T12:40:54Z

Download

← Older revision		Revision as of 08:40, 5 August 2011
Line 42:		Line 42:

	== Download ==		== Download ==

			You can download source code for the ChunkChromosome program from [here]. After downloading it, unpack the archive and use Make to compile the tool.

Goncalo: /* Usage */

2011-08-05T12:06:20Z

Usage

← Older revision		Revision as of 08:06, 5 August 2011
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	</source>		</source>

	The ''autoChunk'', generated by the ChunkChromosome program, tells minimac what are the markers of interest for each chunk. This allows chunks to overlap (which improves accuracy near the edges) but still ensures that each marker is only imputed once.		The ''autoChunk'' file, generated by the ChunkChromosome program, tells minimac what are the markers of interest for each chunk. This allows chunks to overlap (which improves accuracy near the edges) but still ensures that each marker is only imputed once.

	== Download ==		== Download ==