PASS variants only

0.5.1.2

vep fail option

ClinVar fix

• fixed a bug in new ClinVar VCF
• added VEP option --failed

VCF validation

• fixed a bug with VCF validation

VEP update + TOML

• Updated version of VEP (v90)
• Updated versions of ClinVar, Uniprot KB, CIViC, CBMDB
• Removal of ExAC (replaced by gnomAD), removal of COSMIC due to licensing restrictions
• Users can analyze samples run without matching control (i.e. tumor-only)
• PCGR pipeline is now configured through a TOML-based configuration file
• Bug fixes / general speed improvements

vcfanno update

• update vcfanno to v 0.2.8

v0.4.2

• altered docs/help text in some options
• fixed minor bug for allelic depth specification

v0.4.1

• Added a medical disclaimer (research purposes only) to the HTML report
• Added PCGR software version to the report

Allelic support & MSI status

• fixed bugs filed by users
• support for specification of allelic depth/fraction (SNVs/Indels)
• prediction of microsatellite instability
• export of datatables to Excel/CSV
• analysis of MSI/mutational signatures is optional
• improved interactivity of clinical evidence items

v0.3.4

• code documentation

v0.3.3

• automatic decomposition of multiallelic sites
• 'chr' in CHROM column permitted