User contributions
From Genome Analysis Wiki
- 22:12, 5 February 2013 (diff | hist) . . (+122) . . Mach2dat: Association with MACH output (current)
- 07:56, 16 May 2012 (diff | hist) . . (+296) . . Thunder
- 16:13, 24 April 2012 (diff | hist) . . (+12) . . MaCH FAQ (→MaCH-Admix)
- 16:12, 24 April 2012 (diff | hist) . . (+20) . . MaCH FAQ (→MaCH-Admix)
- 15:59, 27 March 2012 (diff | hist) . . (-4) . . MaCH FAQ (→MaCH-Admix)
- 15:58, 27 March 2012 (diff | hist) . . (-2) . . MaCH FAQ (→MaCH-Admix)
- 16:58, 23 February 2012 (diff | hist) . . (0) . . Thunder
- 16:57, 23 February 2012 (diff | hist) . . (-1) . . Thunder (→Input Data)
- 07:31, 2 February 2012 (diff | hist) . . (-2) . . Thunder (→(step 2) Genotype/haplotype calling using thunder thunder_glf_freq)
- 07:31, 2 February 2012 (diff | hist) . . (+17) . . Thunder (→(step 2) Genotype/haplotype calling using thunder thunder_glf_freq)
- 17:38, 15 January 2012 (diff | hist) . . (-2) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 17:38, 15 January 2012 (diff | hist) . . (+344) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 17:38, 13 January 2012 (diff | hist) . . (+7) . . MaCH FAQ (→MaCH-Admix)
- 17:37, 13 January 2012 (diff | hist) . . (+14) . . MaCH FAQ (→MaCH-Admix)
- 17:37, 13 January 2012 (diff | hist) . . (+50) . . MaCH FAQ (→MaCH-Admix)
- 17:36, 13 January 2012 (diff | hist) . . (+428) . . MaCH FAQ (→minimac)
- 16:58, 29 November 2011 (diff | hist) . . (+11) . . MaCH FAQ (→minimac)
- 08:24, 17 November 2011 (diff | hist) . . (+124) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 08:23, 17 November 2011 (diff | hist) . . (+38) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 15:27, 7 November 2011 (diff | hist) . . (0) . . Mach DAC
- 11:20, 3 November 2011 (diff | hist) . . (+108) . . Thunder
- 11:18, 3 November 2011 (diff | hist) . . (+48) . . Thunder
- 20:15, 4 August 2011 (diff | hist) . . (+2) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 21:22, 29 July 2011 (diff | hist) . . (-117) . . MaCH FAQ (→Do I always have to sort the pedigree file by marker position?)
- 21:21, 29 July 2011 (diff | hist) . . (+166) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 15:29, 11 July 2011 (diff | hist) . . (+111) . . Thunder
- 19:07, 19 June 2011 (diff | hist) . . (+201) . . Thunder
- 12:01, 6 June 2011 (diff | hist) . . (+1,391) . . MaCH FAQ (→minimac)
- 20:30, 15 February 2011 (diff | hist) . . (-12) . . MaCH FAQ (→How do I get imputation quality estimates?)
- 14:22, 10 February 2011 (diff | hist) . . (+567) . . Mach DAC (→Split Your Data)
- 06:55, 10 February 2011 (diff | hist) . . (+347) . . Minimac
- 08:43, 8 February 2011 (diff | hist) . . (+28) . . Thunder (→Important Filters)
- 08:41, 8 February 2011 (diff | hist) . . (+39) . . Thunder (→flanking sequence filter)
- 08:38, 8 February 2011 (diff | hist) . . (+166) . . Thunder (→Important Filters)
- 08:37, 8 February 2011 (diff | hist) . . (0) . . Thunder (→total depth filter)
- 08:36, 8 February 2011 (diff | hist) . . (+92) . . Thunder
- 07:01, 28 January 2011 (diff | hist) . . (+589) . . CalcMatch
- 12:53, 15 January 2011 (diff | hist) . . (0) . . MaCH FAQ
- 12:51, 15 January 2011 (diff | hist) . . (+136) . . MaCH FAQ
- 18:04, 11 January 2011 (diff | hist) . . (+74) . . CalcMatch
- 08:53, 9 January 2011 (diff | hist) . . (0) . . Thunder
- 08:53, 9 January 2011 (diff | hist) . . (0) . . Thunder
- 09:29, 7 December 2010 (diff | hist) . . (+93) . . Mach DAC
- 09:27, 7 December 2010 (diff | hist) . . (+10) . . Mach DAC (→Post Phasing/Imputation Ligation)
- 09:27, 7 December 2010 (diff | hist) . . (+94) . . Mach DAC
- 09:19, 7 December 2010 (diff | hist) . . (+2,735) . . N SplitRef (Created page with 'This page documents the splitRef program, which splits a reference haplotype file into smaller files with subsets of markers. == Input Files == === Required Input Files === ====…')
- 09:18, 5 December 2010 (diff | hist) . . (+99) . . MaCH FAQ (→How do I get reference files for an region of interest?)
- 16:18, 29 November 2010 (diff | hist) . . (-95) . . Mach DAC
- 15:33, 29 November 2010 (diff | hist) . . (+414) . . Mach DAC
- 14:52, 29 November 2010 (diff | hist) . . (+109) . . Mach DAC
- 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)…')
