User contributions
2 February 2017
MaCH: Input Files
Optional Phased Haplotypes
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MaCH: Input Files
Optional Phased Haplotypes
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MaCH: Input Files
no edit summary
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MaCH: machX
Reference Haplotypes
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MaCH: machX
Your Own Data
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Thunder
Ligate Haplotypes
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Thunder
Example Showing the Whole Pipeline
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Thunder
(step 2) Genotype/haplotype calling using thunder thunder_glf_freq
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Thunder
(step 1) Site promotion using software glfMultiples GPT_Freq
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Mach DAC
Post Phasing/Imputation Ligation
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Mach DAC
Phasing/Imputation with External Reference
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Mach DAC
Split Your Data
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MaCH FAQ
How do I get imputation quality estimates?
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MaCH FAQ
How do I get imputation quality estimates?
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MaCH FAQ
Install MaCH
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MaCH FAQ
How do I get reference files for an region of interest?
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MaCH FAQ
How do I interpret the imputation quality estimates?
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MaCH FAQ
Where can I find HapMap III / 1000 Genomes reference files?
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MaCH FAQ
Where can I find combined HapMap reference files?
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MaCH FAQ
minimac
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TrioCaller:Archive
no edit summary
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RareSimu
Download
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BamGenotypeCheck
Download bamGenotypeCheck
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Karma
Download Karma
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Template:SeqShopExtSetup
Download the Workshop Example Data
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SeqShop: Sequence Mapping and Assembly Practical, June 2014
Download the example data
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BAM Review Action Items
Useful Links
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C++ Class: SamFileHeader
Sam Header Basics
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C++ Class: SamFileHeader
Sam Header Basics
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C++ Class: SamFile
SamFileWriter
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C++ Class: SamFile
SamFileReader
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C++ Class: SamFile
Class Documentation
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C++ Class: SamRecord
Getting/Setting fields in a SAM/BAM Record
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LibStatGen: GLF
GLF Classes
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FastQValidator
Return Value
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C++ Class: FastQFile
Reading/Validating FastQ Files In Your Program
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LibStatGen: BAM
BAM/SAM Classes
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C++ Class: CigarRoller
CigarRoller
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LibStatGen: general
Genetics Based Classes
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LibStatGen: general
Basic Programming Classes
LibStatGen: FASTQ
Classes in the FASTQ Portion of Library
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C++ Class: InputFile
InputFile Class Documentation
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C++ Class: InputFile
Global IFILE Methods
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SAM/BAM Convert Sequence
Proposed Solution
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SAM/BAM Convert Sequence
Proposed Solution
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TabAnno
Built-in example
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VerifyBamID
Download verifyBamID
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UMAKE
Download UMAKE
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Test EPACTS for DIAGRAM
Download EPACTS
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SeqShop: Genetic Association Analysis Practical, December 2014
Download & Build EPACTS
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