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CNVkit Fix (version 0.9.12+galaxy0)

Sample Target coverage cnn file:

Sample Antitarget coverage cnn file:

Reference coverage cnn file:

TAS-on-target coverage cnn file is also accepted

Compare and use cluster-specific values present in the reference profile:

Sample ID for target/antitarget files:

Otherwise inferred from file names

Skip GC correction:

Skip edge-effect correction:

Skip RepeatMasker correction:

Combine the uncorrected target and antitarget coverage tables (.cnn) and correct for biases in regional coverage and GC content, according to the given reference.

The reference .cnn file output contains those columns chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)