purple-v2.31

Added microsatellite status
Added subclonal likelihood model and figure
Consistent file headers
Consistent file names
Fix whole genome duplication calculation
Changed definition of ref_genome parameter to be mandatory path to reference fasta file.
Added REP_S, REP_C, MH, TNC, KT fields to somatic vcf output
Added REF_G to structural vcf output
Added variant rainfall plot

patient-db-v3.24

load somatic variants no longer needs ref genome

health-checker-v3.1

Bug fix release to support WGSMetrics produced by most recent version of Picard tools

amber-v2.5

Fixed bug in contamination model if absolute zero contamination

patient-db-v3.21

Loads SVs to DB

amber-v2.4

• Added optional snp_bed parameter to output germline snps at specified locations
• Changed file names and headers for better consistency with other HMF tools

sv-linx-v1.0

Linx: updated command line example in read me

purple-v2.30

Removed FittedSegment file and db table
Added wholeGenomeDuplication field to purity output (true if more than 10 autosomes have major allele ploidy > 1.5)
Improved logging of missing arguments
Added support for new AMBER and COBALT file names and formats

health-checker-v3-0

Changes:

• Health checker now evaluates health check and touches either a success or failed file
• Somatic checks have been dropped, amber contamination check is added

purple-v2.29

Add biallelic status to somatic VCF
Removed low VAF SGL filtering logic
Create plot directory before writing to it
Allow plotting of negative copy numbers