Tier assignment fix

• Fixed reported bugs in tier assignment of variants

Python3 + grch38

• Updated data sources
• Enabling specification of tumor type of input sample
• New tier system for classification of variants (ACMG-like)
• VCF validation can be turned off
• Tumor DP/AF presets
• JSON dump of report content
• GRCh38 support
• Runs under Python3

Option fix

Corrects a bug with propagation of default options

v0.5.2

0.5.2 release

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