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Version 0.7.2
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@etal etal released this 09 Oct 20:58
· 1241 commits to master since this release
v0.7.2
b6a7a55

A variety of mostly minor improvements and bug fixes over v0.7.1.

segment, gainloss, segmetrics:

  • Don't exclude very-low-coverage bins from calculations by default; instead,
    expose this option as --drop-low-coverage. (This option usually helps on
    tumor samples with some normal contamination, but leads to problems on
    germline samples with homozygous deletions.)

segment:

  • Output .cns files now have a "weight" column which is the mean of the weights
    of the bins it covers.
  • Output of the 'haar' segmentation method now has each segment's gene names
    listed, as with the other methods.
  • Fixed a bug where every segment's probe count (the "probes" column) could be
    overwritten with the _ character. (#53; thanks @chapmanb)

segmetrics:

  • Each statistic is now printed in its own column, instead of squeezing all
    stats into the "gene" column. The confidence/prediction interval stats get
    two columns, _lo and _hi (lower and upper bound).

loh, scatter:

  • Given a VCF called on a tumor-normal pair, use the paired normal to select
    appropriate germline SNPs for plotting.

export:

  • New format "nexus-ogt" combines bin-level copy number ratios with b-allele
    frequencies given a VCF and a .cnr file. This replaces "nexus-basic" with the
    -v option that was introduced in v0.7.1; "nexus-ogt" stores the same info
    but can be viewed in BioDiscovery Nexus Copy Number without any special
    configuration (load it as the "Custom-OGT" data format).
  • Renamed bed option --show-neutral to --show-all.
  • vcf option -g/--gender now works properly for identifying CNVs on sex
    chromosomes.

call:

  • Fixed the threshold method to calculate absolute copy number on sex
    chromosomes correctly. (#49; thanks @tskir)
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