purple v3.2

Functional:

• increased threshold for low SNV count from 1K to 2K, rename CopyNumber PDF chart to MACN
• check for missense with splice if former reportable and latter not
• apply additional reportable transcripts from driver gene panel file
• write germline deletions to file

Bugs:

• cap hotspot VAF at 0.5 when used for somatic purity
• handle missing genotype (by sample-name) when checking allelic depth
• operate without structural variant VCFs as was previously supported
• added missing Low Tumor VCN VCF header

Gene-related

• handle alt-transcipts for drivers
• use Ensembl data cache instead of all genes TSV (config: ensembl_data_dir)
• handle multiple transcripts per gene in geneCopyNumber
• disable SnpEff annotation when Pave has been run already

Techincal:

• run drivers only (config: drivers_only) if Purple files exist from earlier run
• can run without somatic VCF
• can run without SV VCFs
• optionally use Ensembl data cache instead of built-in gene panel (config: ensembl_data_dir)

Recommended config changes:

• supply Ensembl data cache: ensembl_data_dir
• change driver_catalog to run_drivers