Thunder - Revision history

Ppwhite: /* (step 2) Genotype/haplotype calling using thunder thunder_glf_freq */

2017-02-21T16:08:50Z

(step 2) Genotype/haplotype calling using thunder thunder_glf_freq

← Older revision		Revision as of 12:08, 21 February 2017
Line 27:		Line 27:
	Notes:		Notes:

	(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://sph.umich.edu/csg/~~yli~~/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].		(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://sph.umich.edu/csg/abecasis/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].

	(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://sph.umich.edu/csg/~~yli~~/thunder/thunder.V011.source.tgz thunder_glf_freq].		(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://sph.umich.edu/csg/abecasis/thunder/thunder.V011.source.tgz thunder_glf_freq].

	== Example Showing the Whole Pipeline ==		== Example Showing the Whole Pipeline ==

Ppwhite: /* (step 2) Genotype/haplotype calling using thunder thunder_glf_freq */

2017-02-21T16:06:47Z

(step 2) Genotype/haplotype calling using thunder thunder_glf_freq

← Older revision		Revision as of 12:06, 21 February 2017
Line 27:		Line 27:
	Notes:		Notes:

	(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://~~csg.~~sph.umich.edu//yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].		(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].

	(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://~~csg.~~sph.umich.edu//yli/thunder/thunder.V011.source.tgz thunder_glf_freq].		(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].

	== Example Showing the Whole Pipeline ==		== Example Showing the Whole Pipeline ==

Ppwhite: /* Ligate Haplotypes */

2017-02-02T15:27:22Z

Ligate Haplotypes

← Older revision		Revision as of 11:27, 2 February 2017
Line 35:		Line 35:

	== Ligate Haplotypes ==		== Ligate Haplotypes ==
	Please use [http://~~www~~.sph.umich.edu/~~csg~~/yli/ligateHap.V004.tgz ligateHaplotypes].		Please use [http://csg.sph.umich.edu//yli/ligateHap.V004.tgz ligateHaplotypes].

	== Important Filters ==		== Important Filters ==

Ppwhite: /* Example Showing the Whole Pipeline */

2017-02-02T15:27:06Z

Example Showing the Whole Pipeline

← Older revision		Revision as of 11:27, 2 February 2017
Line 32:		Line 32:

	== Example Showing the Whole Pipeline ==		== Example Showing the Whole Pipeline ==
	In the thunder [https://~~www~~.sph.umich.edu/~~csg~~/yli/thunder/thunder.V011.source.tgz thunder_glf_freq] tarball, you can find under example/thunder/ folder, input files extracted from real data and a C-shell script that executes the whole analysis pipeline.		In the thunder [https://csg.sph.umich.edu//yli/thunder/thunder.V011.source.tgz thunder_glf_freq] tarball, you can find under example/thunder/ folder, input files extracted from real data and a C-shell script that executes the whole analysis pipeline.

	== Ligate Haplotypes ==		== Ligate Haplotypes ==

Ppwhite: /* (step 2) Genotype/haplotype calling using thunder thunder_glf_freq */

2017-02-02T15:26:33Z

(step 2) Genotype/haplotype calling using thunder thunder_glf_freq

← Older revision		Revision as of 11:26, 2 February 2017
Line 21:		Line 21:
	minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.		minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.

	=== (step 2) Genotype/haplotype calling using thunder [https://~~www~~.sph.umich.edu/~~csg~~/yli/thunder/thunder.V011.source.tgz thunder_glf_freq] ===		=== (step 2) Genotype/haplotype calling using thunder [https://csg.sph.umich.edu//yli/thunder/thunder.V011.source.tgz thunder_glf_freq] ===

	thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out		thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
Line 27:		Line 27:
	Notes:		Notes:

	(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://~~www~~.sph.umich.edu/~~csg~~/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].		(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://csg.sph.umich.edu//yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].

	(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://~~www~~.sph.umich.edu/~~csg~~/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].		(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://csg.sph.umich.edu//yli/thunder/thunder.V011.source.tgz thunder_glf_freq].

	== Example Showing the Whole Pipeline ==		== Example Showing the Whole Pipeline ==

Ppwhite: /* (step 1) Site promotion using software glfMultiples GPT_Freq */

2017-02-02T15:25:59Z

(step 1) Site promotion using software glfMultiples GPT_Freq

← Older revision		Revision as of 11:25, 2 February 2017
Line 15:		Line 15:
	This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information.		This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information.

	=== (step 1) Site promotion using software glfMultiples [https://~~www~~.sph.umich.edu/~~csg~~/yli/GPT_Freq.011.source.tgz GPT_Freq] ===		=== (step 1) Site promotion using software glfMultiples [https://csg.sph.umich.edu//yli/GPT_Freq.011.source.tgz GPT_Freq] ===

	GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf		GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf

Ylwtx at 11:56, 16 May 2012

2012-05-16T11:56:13Z

← Older revision		Revision as of 07:56, 16 May 2012
Line 30:		Line 30:

	(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].		(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].

			== Example Showing the Whole Pipeline ==
			In the thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq] tarball, you can find under example/thunder/ folder, input files extracted from real data and a C-shell script that executes the whole analysis pipeline.

	== Ligate Haplotypes ==		== Ligate Haplotypes ==

Ylwtx at 20:58, 23 February 2012

2012-02-23T20:58:18Z

← Older revision		Revision as of 16:58, 23 February 2012
Line 21:		Line 21:
	minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.		minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.

	=== (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.~~V010~~.source.tgz thunder_glf_freq] ===		=== (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq] ===

	thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out		thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
Line 29:		Line 29:
	(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://www.sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].		(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://www.sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki].

	(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder/thunder.~~V010~~.source.tgz thunder_glf_freq].		(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder/thunder.V011.source.tgz thunder_glf_freq].

	== Ligate Haplotypes ==		== Ligate Haplotypes ==

Ylwtx: /* Input Data */

2012-02-23T20:57:50Z

Input Data

← Older revision		Revision as of 16:57, 23 February 2012
Line 9:		Line 9:
	samtools pileup -g -T 1 -f ref.fa my.bam > my.glf		samtools pileup -g -T 1 -f ref.fa my.bam > my.glf

	Note: you will need the reference fasta file ref.fa to create glf file from bam file.		Note: you will need the reference fasta file ref.fa to create glf file from bam file.

	== How to Run ==		== How to Run ==

Ylwtx: /* (step 2) Genotype/haplotype calling using thunder thunder_glf_freq */

2012-02-02T11:31:46Z

(step 2) Genotype/haplotype calling using thunder thunder_glf_freq

← Older revision		Revision as of 07:31, 2 February 2012
Line 23:		Line 23:
	=== (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V010.source.tgz thunder_glf_freq] ===		=== (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V010.source.tgz thunder_glf_freq] ===

	thunder_glf_freq --shotgun my.out.$chr ----detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out		thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out

	Notes:		Notes: