Version 0.6.0

Added two new commands, call and segmetrics, and a new export format, BED.

segmetrics:

• Calculates summary statistics of the residual bin-level log2 ratio estimates from the segment means, similar to the existing metrics command, but for each segment individually. Results are output in the same format as the CNVkit segmentation file (.cns), with the stat names and calculated values printed in the "gene" column.
• Supported stats:
  • standard deviation, median absolute deviation, inter-quartile range, Tukey's biweight midvariance (as in metrics);
  • confidence interval, estimated by bootstrap;
  • prediction interval, estimated by the range between the 2.5-97.5 percentiles of bin-level log2 ratio values within the segment.
• Thanks to @mjafin for suggesting this feature (#28).

call:

• Given segmented log2 ratio estimates (.cns file), round the copy ratio estimates to integer values using either:
  • A list of threshold log2 values for each copy number state, or
  • Some algebra, given known tumor cell fraction and normal ploidy. (This was previously available through the export freebayes command, see below.)
• The output is another .cns file, where the values in the log2 column are still log2-transformed, but represent integers in log2 scale -- e.g. a neutral diploid state is represented as "0.0", not the integer 2. These output files are still compatible with the other CNVkit commands that accept .cns files, and can be plotted the same way.

export bed:

• New bed format supporting the same features as export freebayes that were not moved into the call command (see above). The output BED file is still compatible with the FreeBayes --cnv-map option. In addition, export bed has the new option --show-neutral to also output neutral-CN segments/regions, in addition to the CNV regions output by default.
• The export freebayes sub-command is deprecated but still available in this release; it will be removed in the next release. This command supported the tumor-purity adjustment now implemented in the call command. The recommended approach is to instead run call first on each .cns file, and then export bed on all the adjusted .cns files to get an equivalent BED file compatible with FreeBayes --cnv-map option.

Smaller changes:

• gainloss: Reduced the default log2 ratio threshold from .5 to .2
• import-picard: Use the un-normalized mean coverage instead of the normalized coverage of each target as the log2 coverage values in the output .cnn file. This matches the output of the coverage command; CNVkit normalizes coverages later in the pipeline.
• Some internal refactoring. Please report any bugs, real or perceived, on our GitHub issue tracker.