Canvas 1.40.0.1613+master

fix exception in pedigree caller due to max coverage out of range

Canvas 1.39.0.1598+master

Resolve over-segmentation issue with multiple samples

Canvas 1.38.0.1554+master

This is an update to the Somatic-WGS workflow:

• Split segments when reference ploidy changes
• Use missing GT for CNV calls on chrY in females
• Improvements to purity/ploidy estimation
• Improved handling of low purity samples
• Improved calling of focal amplifications

Canvas 1.35.1.1316+master

• Fix CANV-423: VFResults.txt.gz overwritten by .baf file

• EvaluteCNV: skip non-CNV calls when calculating variant events and variant bases

• Fix to variant events/variant bases calculation: use majority overlap with reference ploidy regions to determine if call is variant

Canvas 1.35.0.1280+master

• EvaluateCNV: use bit array to load kmer fasta with less memory

• Fix to partitioning (#369)

• EvaluateCNV: fix to median and mean accuracy calculations (#373)

• Fix to MCC calculation for a pedigree (CANV-533)

• EvaluateCNV: use all truth intervals even if there are no overlapping Canvas calls (CANV-548)

• Double denovo quality score so that the new threshold is 20 rather than 10 (#378) (SPW-1443)

• Fix to partitioning: remove use of MeanSmoother (#379)

• EvaluateCNV: Fix accuracy calculation (#376)

Canvas 1.34.0.1201+master

• L10kb filter
• EvaluateCNV updated to handle reference ploidy without requiring a ploidy.vcf.gz
• Provide (higher resolution) CANVAS depth as wig/bg/bigwig under [outdir]/VisualizationTemp[samplename] subfolder
• Sibling tag support, support for mixed input of trio and other sample types
• Updated format includes CN0, CN2 etc. in ALT column
• Bug fixes in de-novo scoring model
• per-sample filter tag in a multi-sample VCF file

Canvas 1.32.0.918+master

1.32.0.918+master

Canvas 1.31.0.843+master

Bug fixes:

Key	Component/S	Summary
CANV-476	Germline-WGS, SmallPedigree-WGS	malformatted VCF
CANV-473	SmallPedigree-WGS	failure on single proband sample
CANV-467	SmallPedigree-WGS	Duo dataset failed at Canvas step

 
Improvements:

Key	Component/S	Summary
CANV-352	SmallPedigree-WGS	Add FT (filter) sample tag to multi-sample and single sample VCF output
CANV-461		Add <CNX> information to GT sub-field
CANV-451		Update SNVReviewer to accept GQX < 30 when variant is PASS (including FT field)

Canvas 1.30.0.725+master

1.30.0.725+master

Canvas 1.28.0

1.28.0.272

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