Version 0.7.10
diagram:
- Label genes even when given only segments (.cns). Plotting segments alone,
without bin-level copy ratios (.cnr), can be convenient to produce an
uncluttered PDF with a smaller file size while retaining most of the important
CNV information.
scatter:
- For calculating and plotting SNV b-allele frequencies, select the sample of
interest from the given VCF based on the .cnr/.cns base filename, unless
specified with `--sample-id`.
export nexus-ogt:
- Use normal-sample BAFs if normal-sample .cnr given. Previously, it would load
tumor BAFs (taking the first tumor sample from the PEDIGREE tag) even if the
properly-named .cnr file was for the normal sample in the VCF.
- Add --sample-id option to select VCF sample. Useful in case .cnr filename base
doesn't match the sample IDs in the VCF header.
- Add filtering options --min-weight, --min-variant-depth.
- The `--min-variant-depth` option works the same as in `scatter -v`,
filtering SNVs by coverage depth (INFO field DP, usually) for the b-allele
frequency calculation.
- The `--min-weight` option allows the user to discard low-weight bins since
Nexus Copy Number doesn't use CNVKit's weights for its own segmentation
and could be misled by the noisier log2 ratios in less-reliable bins. For
choosing the cutoff value, 0.5 is suitable in our experience, but check
the distribution of weights in your own data first.
export vcf:
- Add custom VCF "FORMAT" fields: FOLD_CHANGE, FOLD_CHANGE_LOG2, PROBES. (#91;
thanks @pcingola)
segment:
- The "flasso" method now works again; it was broken for a few releases. (#88; thanks
@pcingola)
Packaging & internal:
- Add GRCh37 "access" BED file for users' convenience. The `access` command will
also now raise an error if the chromosome names don't match between the
"access" and "target" BED files.
- Work with the latest version of pysam (0.9). (#86)
- Silence some superfluous warnings from the latest version of pandas (0.18).
- Documentation updates, including more details on the `call` command.