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Jump to navigationJump to searchUnderstanding VerifyBamID output (view source)
Revision as of 16:46, 4 March 2013
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=Example VerifyBamID Output=
== Expected Output from verifyBamID ==
This section explains the expected output from [[verifyBamID]] software. See [[VerifyBamID#Interpreting_output_files|VerifyBamID output documentation]] for more details.
There will be four types of files produced by [[verifyBamID]]
* *.genoCheck.depthRG
* *.selfSM : Main output file containing the contamination estimate. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if available)
* *.genoCheck.depthSM
* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)
* *.genoCheck.selfRG
* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.
* *.genoCheck.selfSM
* *.depthRG : : The depth distribution of reads covering the marker position of the input VCF, per readGroups.
== VerifyBamID Tutorial Output ==
== VerifyBamID Tutorial Output ==
