4.4.1: Updated to take advantage of htslib 1.11+libdeflate

Performance improvements.

4.4.0

Generation of the counts files can now be on a per-sample process, separated from the full ascat.pl run.

New script: ascatCounts.pl

ascat.pl can now start from a pair of count files instead of the BAM/CRAM files, some additional parameters are required for data previously pulled from the BAM/CRAM header.

v4.1.2 - Hotfix v4.1.1 with use of tabix->query_full

Change tabix->query to use tabix->query_full

v4.2.1 - Update to tabix call

4.2.1

• Update tabix call to use query_full

v4.2.0 - ASCAT.R fix and upgrade of dep recommended

• Upgrade to core R ASCAT v2.5.1
  • applies patch to handle sparse data on a contig (usually Human Y)
• Recommend upgrading to alleleCount v4.0.0+
  • Switches to fragment based counts instead of read based to prevent double counting.

v4.1.0

• Uses new alleleCounter -d option to speed up allele counting step

v4.0.0 - BigWig files for GenomeBrowsers

Now generates 7 additional files by default:

X.copynumber.baf.bw
X.copynumber.logR.bw
X.copynumber.minorCn.bw
X.copynumber.rawCn.bw
X.copynumber.segBaf.bw
X.copynumber.segLogR.bw
X.copynumber.totalCn.bw

This behaviour is optional (and requires cgpBigWig). To disable add -nb to your command.

JBrowse example displays:

LogR

BAF

CN

JBrowse config
Using the MultiBigWig plugin:

{
  "storeClass" : "MultiBigWig/Store/SeqFeature/MultiBigWig",
  "max_score" : 1,
  "min_score" : -1,
  "style": { "height": 100 },
  "urlTemplates" : [
    {"url":"ascat/X.copynumber.logR.bw","name":"logR", "color": "grey", "nonCont": true},
    {"url":"ascat/X.copynumber.segLogR.bw","name":"segLogR", "color": "green", "nonCont": true}
  ],
  "showTooltips": true,
  "label" : "ascatLogR",
  "type" : "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
},
{
  "storeClass" : "MultiBigWig/Store/SeqFeature/MultiBigWig",
  "max_score" : 1,
  "min_score" : 0,
  "style": { "height": 100 },
  "urlTemplates" : [
    {"url":"ascat/X.copynumber.baf.bw","name":"BAF", "color": "grey", "nonCont": true},
    {"url":"ascat/X.copynumber.segBaf.bw","name":"segBAF", "color": "green", "nonCont": true}
  ],
  "showTooltips": true,
  "label" : "ascatBAF",
  "type" : "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
},
{
  "storeClass" : "MultiBigWig/Store/SeqFeature/MultiBigWig",
  "max_score" : 10,
  "min_score" : 0,
  "style": { "height": 100 },
  "urlTemplates" : [
    {"url":"ascat/X.copynumber.rawCn.bw","name":"rawCn", "color": "grey", "nonCont": true},
    {"url":"ascat/X.copynumber.totalCn.bw","name":"totalCn", "color": "green", "nonCont": true},
    {"url":"ascat/X.copynumber.minorCn.bw","name":"minorCn", "color": "red", "nonCont": true},
  ],
  "showTooltips": true,
  "label" : "ascatCn",
  "type" : "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
}

Travis-CI and install fix

• Adds Travis support
• Fixes an issue in later versions of perl and issues in setup.sh

v3.0.3 - Handle very poor input

Further handling of bad input data.

Now provides additional information if ASCAT fails to generate data for sunrise purity/ploidy estimates. This is most commonly associated with attempting to use an unmatched normal sample.

Also gzips the copynumber.txt file.

v3.0.2 - minor bugfix release

Changes:

• Utility scripts now installed
• ascatSnpPanelGenerator.pl handles absence of -exclude option correctly (highly inadvisable to omit)