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To get a copy of older releases go to the [http://www.sph.umich.edu/csg/kang/verifyBamID/download VerifyBamID Download] download page.
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 ==
# 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.
# RDPHET : DPHET/DPREF, Relative depth at Heterozygous site.
# RDPHET : DPHET/DPREF, Relative depth to HomRef site at Heterozygous site.
# RDPALT : DPHET/DPREF, Relative depth at HomAlt site.
# RDPALT : DPHET/DPREF, Relative depth to HomRef site at HomAlt site.
=== A guideline to interpret output files ===
=== A guideline to interpret output files ===
* --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
* --free-mix : (default) Estimate contamination using sequence+array method with Brent's single dimensional optimization.
* --chip-mix : (default) Estimate contamination using sequence+array method with Brent's single dimensional optimization.
* --free-refBias : Estimate the refernece bias parameters using sequence+array method with Simplex method
* --chip-refBias : Estimate the refernece bias parameters using sequence+array method with Simplex method
* --free-full : Estimate both reference bias parameters and the contamination parameters using sequence+array method
* --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)
== Acknowledgements ==
== Acknowledgements ==
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.
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.
