purple v4.0

Functional:

• don’t fit short arms on 13,14,15,21,22
• Mask IG/TCR regions in fit
• Mask regions <2MB from centromere in fit
• Where ambiguous (low purity), BAF is now fit to minimise major allele CN
• chromosome X CN amplifications are called at 1.5x ploidy for males
• don’t smooth large germline deletions in diploid normalisation logic
• fit in 0.5% intervals for purity <20% and lower min to 7%
• write list of reportable transcripts to somatic VCF when alt-transcripts (eg CDKN2A) exist for a driver gene
• add LOH percent to QC output file

Technical:

• allow extra sample IDs in VCF and any order
• throw exception and exit on charting error

Bugs:

• ploidy was not calculated accurately in somatic mode

Visualisations

• only show diploid regions in input.png
• tumor is always in blue in input.png

Panel:

• add deviation penalty adjustment for GC ratio (config: gc_ratio_exponent, deviation_penalty_gc_min_adjust)
• set targeted panel default values:
  -ploidy_penalty_standard_deviation 0.10
  -ploidy_penalty_min 0.20
  -ploidy_penalty_sub_one_major_allele_multiplier 3.00
  -deviation_penalty_gc_min_adjust 0.25
  -gc_ratio_exponent 3.0
  -min_diploid_tumor_ratio_count 3
  -min_diploid_tumor_ratio_count_centromere 3