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Version 0.7.10
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@etal etal released this 06 Apr 21:08
· 1050 commits to master since this release
v0.7.10
4da7808

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. (#94)

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.
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