Releases · molgenis/CoNVaDING

The following bugs have been fixed in the update from version 1.1.6 to v1.2.0:+

Major:

In version 1.1.6 after running the StartWithBam function analyzing a region having a coverage of 0, the normalized coverage would have a value of -NaN. This issue is fixed in version 1.2.0, by adding the -a flag to the samtools depth function. However, this causes a dependency on samtools version 1.3 or higher.
In version 1.1.6 HOM_DEL and HOM_DUP calls were interpreted as separate events as DEL and DUP calls.
This could cause calls to be cut into several pieces and create gaps in the calls because of downstream filtering. Now, HOM_DEL calls are interpreted as part of a DEL call as well as a separate call. For instance if exons 1 and 3 have a DEL call in the totallist and exon 2 a HOM_DEL call. A deletion of exons 1 to 3 will be called as well as a homozygous deletion of exon 2. Similarly HOM_DUP events are considered as part of DUP events as well as a separate call. Note that in case all targets of a call are considered HOM_DEL or HOM_DUP the call will appear twice on the longlist, shortlist and/or finallist.

Minor:

In the StartWithMatchScore function the 'Avg abs diff incl sex' was showing the same value as the 'Avg abs diff autosomal'. Now the values are correct.
A bedfile containing UCSC style notation 'chr1, chr2, etc.' is now be compatible with a header notation of '1, 2, etc.'
The finallist is now called finallist.txt instead of shortlist.finallist.txt.
In the log file produced during the StartWithBestScore function SAMPLE_RATIO has been renamed SAMPLE_CV.
The inputDir is not a requirement anymore for the GenerateTargetQCList function.
In the GenerateTargetQC function the searchpattern is changed to prevent the step trying to process files other than normalized coverage files.
The used commandline options and values are now printed to the stdout by default.

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