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VerifyBamID (view source)

Revision as of 15:29, 9 September 2017

1,438 bytes added ,  15:29, 9 September 2017
→‎Command Line Options
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== Download verifyBamID  ==
 
== Download verifyBamID  ==
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To get a copy go to the [http://www.sph.umich.edu/csg/kang/verifyBamID/download VerifyBamID Download] download page.
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To get a copy of verifyBamId, go to: https://github.com/statgen/verifyBamID/releases
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Select the latest release and download in one of 3 ways:
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# Binary expected to run in Ubuntu x64 platform. In other platforms, please download the source distribution and build it.
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#* verifyBamID.#.#.#.gz
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#* You will need to run "gunzip" on the .gz file
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# Souce Code including libStatGen (uses a fixed version of libStatGen)
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#* verifyBamIDLibStatGen.#.#.#.tgz
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#* Run "tar xvf" on this file.  Cd into the resulting directory & type make.
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# Source Code without libStatGen (allows alternative/newer versions of libStatGen)
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#* Source code (tar.gz) or Source code (zip)
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#* You will need to download libStatGen separately if you do not already have it.
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To get a copy of older releases go to the [http://csg.sph.umich.edu//kang/verifyBamID/download VerifyBamID Download] download page.
    
== Join in verifyBamID mailing list ==
 
== Join in verifyBamID mailing list ==
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== What's new ==
 
== What's new ==
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(2014/02/13)
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* Put verifyBamID in github.
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* Added PhoneHome/Version Checking to VerifyBamID
    
(2012/06/20)  
 
(2012/06/20)  
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== Build verifyBamID  ==
 
== Build verifyBamID  ==
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The binary download of verifyBamID is available. You may use the version in Ubuntu 64-bit platform. To build verifyBamID, download the statgen library and run the following series of commands
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The binary download of verifyBamID is available. You may use that version in Ubuntu 64-bit platform.  
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  tar xzvf verifyBamID.20120620.tar.gz
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  cd verifyBamID
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If you download the source that includes libStatGen:
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  make cloneLib (in the case ../libStatGen does not exist)
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tar xvf verifyBamIDLibStatGen.#.#.#.tgz
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cd verifyBamID_#.#.#
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make
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Executable: verifyBamID/bin/verifyBamID
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If you download the source without libStatGen:
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  tar xvf verifyBamID-#.#.#.tar.gz
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  cd verifyBamID-1.1.0
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  make cloneLib (if ../libStatGen does not exist)
 
  make
 
  make
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  ./bin/verifyBamID
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  Executable: ./bin/verifyBamID
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Note that '''make cloneLib''' command will create a directory ../libStatGen under your verifyBamID directory, and '''make''' will create binary of verifyBamID under verifyBamID/bin/
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If you have a different version of libStatGen at that path, then skip the cloneLib step.  If the libStatGen you want to use is at a different location then update verifyBamID's Makefile.inc.  Replace: LIB_PATH_VERIFY_BAM_ID ?= $(LIB_PATH_GENERAL) with
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LIB_PATH_VERIFY_BAM_ID = /path/to/libStatGen
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Note that '''git clone''' command will create a directory ./libStatGen under your working directory, and '''make''' will create binary of verifyBamID under verifyBamID/bin/
      
verifyBamID is designed to be reasonably portable.  
 
verifyBamID is designed to be reasonably portable.  
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However, since development occurs only on Ubuntu 9.10 x86 and x64 platforms, and later, there are likely other portability issues.  
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However, since development occurs only on Ubuntu (9.10-13.10) x86 and x64 platforms, and later, there are likely other portability issues.  
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Currently we support verifyBamID only on Ubuntu 9.10 and later on 64-bit processors.
      
== Basic Usage ==
 
== Basic Usage ==
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== Interpreting output files ==
 
== Interpreting output files ==
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See also [[Understanding VerifyBamID output]].
    
=== Output files ===
 
=== Output files ===
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# FREEMIX : Sequence-only estimate of contamination (0-1 scale)
 
# FREEMIX : Sequence-only estimate of contamination (0-1 scale)
 
# FREELK1 : Maximum log-likelihood of the sequence reads given estimated contamination under sequence-only method
 
# FREELK1 : Maximum log-likelihood of the sequence reads given estimated contamination under sequence-only method
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# FREELK0 : Log-ikelihood of the sequence reads given no contamination under sequence-only method
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# FREELK0 : Log-likelihood of the sequence reads given no contamination under sequence-only method
 
# FREE_RH : Estimated reference bias parameter Pr(refBase|HET) (when --free-refBias or --free-full is used)
 
# FREE_RH : Estimated reference bias parameter Pr(refBase|HET) (when --free-refBias or --free-full is used)
 
# FREE_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --free-refBias or --free-full is used)
 
# FREE_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --free-refBias or --free-full is used)
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# CHIP_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --chip-refBias or --chip-full is used)
 
# CHIP_RA : Estimated reference bias parameter Pr(refBase|HOMALT) (when --chip-refBias or --chip-full is used)
 
# DPREF : Depth (Coverage) of HomRef site (based on the genotypes of (SELF_SM/BEST_SM), passing mapQ, baseQual, maxDepth thresholds.
 
# DPREF : Depth (Coverage) of HomRef site (based on the genotypes of (SELF_SM/BEST_SM), passing mapQ, baseQual, maxDepth thresholds.
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# RDPHET : DPHET/DPREF, Relative depth at Heterozygous site.
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# RDPHET : DPHET/DPREF, Relative depth to HomRef site at Heterozygous site.
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# RDPALT : DPHET/DPREF, Relative depth at HomAlt site.
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# RDPALT : DPHET/DPREF, Relative depth to HomRef site at HomAlt site.
    
=== A guideline to interpret output files ===
 
=== A guideline to interpret output files ===
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                                           --refAlt [0.00]
 
                                           --refAlt [0.00]
 
                           Output options : --out [], --verbose
 
                           Output options : --out [], --verbose
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                              PhoneHome : --noPhoneHome,
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                                          --phoneHomeThinning [50]
    
Each option provides the following features:
 
Each option provides the following features:
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* --free-none : Do not perform sequence-only method to estimate parameters
 
* --free-none : Do not perform sequence-only method to estimate parameters
 
* --free-mix : (default) Estimate contamination using sequence-only method with Brent's single dimensional optimization.
 
* --free-mix : (default) Estimate contamination using sequence-only method with Brent's single dimensional optimization.
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* --free-refBias : Estimate the refernece bias parameters using sequence-only method with Simplex method
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* --free-refBias : Estimate the reference bias parameters using sequence-only method with Simplex method
 
* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence-only method
 
* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence-only method
 
* --chip-none : Do not perform sequence+array method to estimate parameters
 
* --chip-none : Do not perform sequence+array method to estimate parameters
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* --free-mix : (default) Estimate contamination using sequence+array method with Brent's single dimensional optimization.
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* --chip-mix : (default) Estimate contamination using sequence+array method with Brent's single dimensional optimization.
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* --free-refBias : Estimate the refernece bias parameters using sequence+array method with Simplex method
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* --chip-refBias : Estimate the refernece bias parameters using sequence+array method with Simplex method
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* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence+array method
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* --chip-full : Estimate both reference bias parameters and the contamination parameters using sequence+array method
 
* --ignoreRG : ignore the read grouup level comparison and compare samples only (recommended for an expedited run)
 
* --ignoreRG : ignore the read grouup level comparison and compare samples only (recommended for an expedited run)
 
* --ignoreOverlapPair : ignore overlapping pair end fragment covering the same base. Disabling this option may decrease the sensitivity of the method when the insert size is short (with slight gain in the computational speed)
 
* --ignoreOverlapPair : ignore overlapping pair end fragment covering the same base. Disabling this option may decrease the sensitivity of the method when the insert size is short (with slight gain in the computational speed)
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* --out : output file prefix (required)
 
* --out : output file prefix (required)
 
* --verbose : print the progress of the method on the screeen
 
* --verbose : print the progress of the method on the screeen
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{{PhoneHomeParameters|hdr=====|bullet=1}}
    
== Principle of Operation ==
 
== Principle of Operation ==
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== For array intensity data ==
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== Contamination in Array Data ==
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[[VerifyIDintensity]] software can estimate sample contamination from Illumina genotype array intensity data.
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[[VerifyIDintensity]] or [[BAFRegress]] can estimate sample contamination from Illumina genotype array data.
    
== Acknowledgements ==
 
== Acknowledgements ==
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VerifyBamID is a result from collaborative effort by Hyun Min Kang, Goo Jun, Matthew Flickinger, Mary Kate Wing, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
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VerifyBamID is a result from collaborative effort by Hyun Min Kang, Goo Jun, Matthew Flickinger, Mary Kate Wing, Goncalo Abecasis, and Michael Boehnke. Please email to Hyun Min Kang [hmkang@umich.edu ] for any questions.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/6563...14829"

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