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Jump to navigationJump to searchUnderstanding VerifyBamID output (view source)
Revision as of 16:48, 4 March 2013
, 16:48, 4 March 2013→Expected Output from verifyBamID
There will be four types of files produced by [[verifyBamID]]
There will be four types of files produced by [[verifyBamID]]
* '''*.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)
* '''*.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 provided)
* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)
* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)
* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.
* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.
