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, 16:47, 4 March 2013
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| 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 available) |
| * *.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. |