User contributions
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Jump to navigationJump to search- 14:42, 29 November 2010 diff hist +181 SplitPed →Example Commands
- 14:40, 29 November 2010 diff hist +123 SplitPed
- 14:39, 29 November 2010 diff hist +140 SplitPed →Example Commands
- 14:36, 29 November 2010 diff hist +781 SplitPed
- 14:28, 29 November 2010 diff hist +2,398 N SplitPed Created page with 'This page documents the splitPed program, which splits a pedigree file into smaller files with subsets of markers. == Input Files == === Required Input Files === ==== Pedigree f…'
- 12:50, 29 November 2010 diff hist +660 Mach DAC
- 08:29, 29 November 2010 diff hist +437 MaCH: machX
- 08:27, 29 November 2010 diff hist +74 Thunder
- 08:22, 29 November 2010 diff hist +140 MaCH FAQ
- 21:13, 28 November 2010 diff hist +4 MaCH FAQ →Why and how to perform a 2-step imputation?
- 21:12, 28 November 2010 diff hist +167 N Mach DAC Created page with 'This is the MaCH Divide and Conquer page, documenting how to break the genome into smaller pieces before imputation/phasing and how to ligate after imputation/phasing.'
- 21:10, 28 November 2010 diff hist +642 MaCH FAQ
- 21:05, 28 November 2010 diff hist -1 MaCH FAQ →Why and how to perform a 2-step imputation?
- 21:04, 28 November 2010 diff hist +59 MaCH FAQ →Why and how to perform a 2-step imputation?
- 09:49, 26 November 2010 diff hist +281 MaCH: machX →Impute
- 09:47, 26 November 2010 diff hist +260 MaCH: machX →Phase Your Own Data
- 09:44, 26 November 2010 diff hist -11 MaCH: machX →Reference Haplotypes
- 09:44, 26 November 2010 diff hist +12 MaCH: machX
- 09:43, 26 November 2010 diff hist +12 MaCH: machX
- 09:42, 26 November 2010 diff hist -1 MaCH: machX
- 09:41, 26 November 2010 diff hist 0 MaCH: machX
- 09:40, 26 November 2010 diff hist +1,018 N MaCH: machX Created page with 'This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [http://www.sph.umich.edu/csg/yli/mach] and minimac [http://genome.sph.umich.edu…'
- 08:34, 26 November 2010 diff hist 0 MaCH current
- 08:33, 26 November 2010 diff hist +42 MaCH
- 07:17, 24 November 2010 diff hist +5 MaCH FAQ →How do I get reference files for an region of interest?
- 16:36, 19 November 2010 diff hist +33 MaCH FAQ →How long does imputation take?
- 18:22, 21 October 2010 diff hist +1 Haploxt →--r2Threshold or -t current
- 18:22, 21 October 2010 diff hist +34 Haploxt
- 18:20, 21 October 2010 diff hist +307 Haploxt →download
- 18:11, 21 October 2010 diff hist -1 Haploxt →.freq
- 18:10, 21 October 2010 diff hist +516 Haploxt
- 18:05, 21 October 2010 diff hist -2,290 Haploxt
- 13:31, 21 October 2010 diff hist +369 Haploxt
- 09:57, 21 October 2010 diff hist +35 Haploxt
- 09:56, 21 October 2010 diff hist +857 Haploxt
- 09:52, 21 October 2010 diff hist +4,021 N Haploxt Created page with 'haploxt is a C/C++ software developed by [https://www.sph.umich.edu/csg/yli/ Yun Li] and [https://www.sph.umich.edu/csg/abecasis/ Goncalo Abecasis]. It calculates LD (D' and r<su…'
- 09:34, 21 October 2010 diff hist +37 CalcMatch
- 16:04, 15 October 2010 diff hist +12 Thunder
- 15:59, 15 October 2010 diff hist +198 Thunder
- 15:56, 15 October 2010 diff hist +60 Thunder
- 15:56, 15 October 2010 diff hist +413 Thunder
- 15:51, 15 October 2010 diff hist +246 Thunder
- 15:48, 15 October 2010 diff hist +16 Thunder
- 15:41, 15 October 2010 diff hist +1 Thunder
- 15:40, 15 October 2010 diff hist +15 Thunder
- 15:40, 15 October 2010 diff hist +177 Thunder
- 15:29, 15 October 2010 diff hist +109 Thunder
- 15:22, 15 October 2010 diff hist +348 Thunder
- 15:17, 15 October 2010 diff hist +75 Thunder
- 13:12, 15 October 2010 diff hist +112 Thunder
- 13:02, 15 October 2010 diff hist +77 Thunder
- 12:43, 15 October 2010 diff hist +413 Thunder
- 12:32, 15 October 2010 diff hist +87 Thunder
- 12:32, 15 October 2010 diff hist +251 Thunder
- 10:34, 15 October 2010 diff hist +296 N Thunder Created page with 'This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. == Input Data == To get started, you will need bam files in…'
- 05:16, 8 August 2010 diff hist +84 MaCH FAQ →undefined symbol: gzopen64
- 22:35, 28 June 2010 diff hist +278 MaCH Options current
- 07:47, 24 June 2010 diff hist +24 MaCH FAQ →How do I interpret the imputation quality estimates?
- 07:47, 24 June 2010 diff hist -33 MaCH FAQ →How do I interpret the imputation quality estimates?
- 07:45, 24 June 2010 diff hist 0 N File:Figure3.pdf current
- 07:44, 24 June 2010 diff hist +993 MaCH FAQ →How do I get imputation quality estimates?
- 07:29, 24 June 2010 diff hist +55 MaCH FAQ →How do I get imputation quality estimates?
- 15:02, 23 June 2010 diff hist +154 MaCH FAQ
- 23:00, 22 June 2010 diff hist -1 CalcMatch
- 22:59, 22 June 2010 diff hist -1 m CalcMatch →example command lines
- 22:59, 22 June 2010 diff hist +866 CalcMatch →example command lines
- 22:55, 22 June 2010 diff hist +6 CalcMatch
- 22:52, 22 June 2010 diff hist +24 CalcMatch
- 22:51, 22 June 2010 diff hist +6 CalcMatch
- 22:51, 22 June 2010 diff hist +116 CalcMatch
- 22:49, 22 June 2010 diff hist +3,176 N CalcMatch Created page with 'CalcMatch is a C/C++ software developed by Yun Li that compares two sets of pedigree files. It was initially written to compare imputed genotypes with their true/experimental cou…'
- 02:11, 17 June 2010 diff hist +362 N MaCH Options Created page with '== greedy == use only the reference haplotypes (fed to -h or --haps) as reference == states S == use a random subset of S haplotypes as reference == sampleInterval SI == out…'
- 02:07, 17 June 2010 diff hist +32 MaCH
- 17:35, 9 June 2010 diff hist +146 MaCH FAQ
- 09:35, 9 June 2010 diff hist +88 MaCH FAQ →How long does imputation take?
- 09:34, 9 June 2010 diff hist +153 MaCH FAQ →Why and how to perform a 2-step imputation?
- 09:32, 9 June 2010 diff hist +112 MaCH FAQ →How long does imputation take?
- 10:55, 4 June 2010 diff hist +190 MaCH: Input Files →Optional Phased Haplotypes
- 09:52, 4 June 2010 diff hist +180 MaCH →HapMap format reference files
- 10:48, 25 May 2010 diff hist +14 MaCH
- 10:47, 25 May 2010 diff hist +25 MaCH
- 10:46, 25 May 2010 diff hist +42 MaCH
- 10:45, 25 May 2010 diff hist +501 MaCH
- 10:21, 25 May 2010 diff hist +110 MaCH
- 15:39, 24 May 2010 diff hist -71 MaCH
- 15:38, 24 May 2010 diff hist +78 MaCH →More questions?
- 15:03, 24 May 2010 diff hist +107 MaCH
- 15:02, 24 May 2010 diff hist +15 MaCH
- 15:01, 24 May 2010 diff hist +2 MaCH
- 15:00, 24 May 2010 diff hist -21 MaCH
- 14:59, 24 May 2010 diff hist -30 MaCH
- 14:58, 24 May 2010 diff hist +1,162 MaCH
- 08:16, 21 May 2010 diff hist +461 MaCH
- 15:50, 20 May 2010 diff hist +20 MaCH
- 15:49, 20 May 2010 diff hist -36 MaCH
- 15:46, 20 May 2010 diff hist 0 MaCH
- 15:46, 20 May 2010 diff hist -6 MaCH
- 15:45, 20 May 2010 diff hist +8 MaCH
- 15:43, 20 May 2010 diff hist +14 MaCH
- 15:43, 20 May 2010 diff hist +163 MaCH
- 15:41, 20 May 2010 diff hist +667 MaCH
- 15:35, 20 May 2010 diff hist +5 MaCH
- 15:35, 20 May 2010 diff hist +540 MaCH
- 15:30, 20 May 2010 diff hist +13 MaCH
- 16:15, 18 May 2010 diff hist +48 MaCH
- 08:01, 18 May 2010 diff hist +6 MaCH →FAQ
- 08:01, 18 May 2010 diff hist +928 MaCH
- 20:55, 17 May 2010 diff hist +1,342 MaCH
- 15:26, 5 May 2010 diff hist +197 MaCH
- 10:08, 3 May 2010 diff hist +8 MaCH
- 10:07, 3 May 2010 diff hist +244 MaCH
- 15:12, 30 April 2010 diff hist +27 MaCH
- 15:11, 30 April 2010 diff hist +93 MaCH
- 15:11, 30 April 2010 diff hist +20 MaCH
- 15:10, 30 April 2010 diff hist +8 MaCH
- 15:10, 30 April 2010 diff hist +3 MaCH
- 15:09, 30 April 2010 diff hist -10 MaCH
- 15:08, 30 April 2010 diff hist +634 MaCH
- 18:05, 26 April 2010 diff hist +2 MaCH
- 18:04, 26 April 2010 diff hist +60 MaCH
- 18:03, 26 April 2010 diff hist +5 MaCH
- 18:03, 26 April 2010 diff hist 0 MaCH
- 18:03, 26 April 2010 diff hist +4 MaCH
- 18:02, 26 April 2010 diff hist -64 MaCH
- 18:02, 26 April 2010 diff hist +144 MaCH
- 18:00, 26 April 2010 diff hist +26 MaCH
- 17:59, 26 April 2010 diff hist +60 MaCH
- 17:58, 26 April 2010 diff hist +36 MaCH
- 17:55, 26 April 2010 diff hist +14 MaCH
- 17:55, 26 April 2010 diff hist +3 MaCH
- 17:53, 26 April 2010 diff hist +5 MaCH
- 17:52, 26 April 2010 diff hist -20 MaCH
- 17:52, 26 April 2010 diff hist -3 MaCH
- 17:51, 26 April 2010 diff hist +1,165 MaCH
- 17:48, 26 April 2010 diff hist +24 MaCH
- 17:48, 26 April 2010 diff hist +41 MaCH
- 17:47, 26 April 2010 diff hist +18 MaCH
- 17:46, 26 April 2010 diff hist +30 MaCH
- 17:46, 26 April 2010 diff hist +1,907 MaCH
- 17:41, 26 April 2010 diff hist +21 MaCH
- 17:40, 26 April 2010 diff hist +93 MaCH
- 17:39, 26 April 2010 diff hist +20 MaCH
- 17:39, 26 April 2010 diff hist +1 MaCH
- 17:38, 26 April 2010 diff hist +16 MaCH
- 17:38, 26 April 2010 diff hist +1 MaCH
- 17:37, 26 April 2010 diff hist +17 MaCH
- 17:37, 26 April 2010 diff hist +19 MaCH
- 17:36, 26 April 2010 diff hist -7 MaCH
- 17:36, 26 April 2010 diff hist +7 MaCH
- 17:35, 26 April 2010 diff hist +528 MaCH
- 17:28, 26 April 2010 diff hist -1 MaCH
- 17:26, 26 April 2010 diff hist +353 MaCH
- 17:22, 26 April 2010 diff hist +26 MaCH
- 17:21, 26 April 2010 diff hist +88 N MaCH Created page with ''''MaCH''' (MArkov Chain Haplotyping) is a software for phasing and genotype imputation.'
- 13:35, 10 March 2010 diff hist 0 1000 Genomes Project Pilot 1 SNP Calling →(3) Build a list of individuals within each population current
- 13:34, 10 March 2010 diff hist +1 1000 Genomes Project Pilot 1 SNP Calling →(2) Split GLF files by chromosome
- 13:32, 10 March 2010 diff hist +864 1000 Genomes Project Pilot 1 SNP Calling →(10) Run thunder (hidden Markov model)
- 13:23, 10 March 2010 diff hist -5 1000 Genomes Project Pilot 1 SNP Calling →=
- 13:21, 10 March 2010 diff hist +46 1000 Genomes Project Pilot 1 SNP Calling →(10) Run thunder (hidden Markov model)
- 13:14, 10 March 2010 diff hist +80 1000 Genomes Project Pilot 1 SNP Calling
- 11:40, 16 February 2010 diff hist +47 Main Page
- 11:36, 16 February 2010 diff hist +7,104 N 1000 Genomes Project Pilot 1 SNP Calling Created page with 'Michigan Pilot One SNP calling work flow: (1) Create GLF files from BAM files (2) Split GLF files by chromosome (3) Build a list of individuals within each population (4)…'