PharmCAT v3.3.0 Released
We are excited to announce our latest release!
This update is highly recommended. It fixes an issue with pharmcat_pipeline where it uses the original input VCF instead of the preprocessed VCF if it is given a directory instead of a file.
Data highlights
- PharmVar: new alleles were released for CYP2C9, CYP2D6, CYP3A4, CYP3A5, NUDT15
- ClinPGx:
- updates released/published for the CPIC Guideline for RYR1, CACNA1S and Volatile anesthetic agents and Succinylcholine and the CPIC Guideline for CYP2D6 and Ondansetron and Tropisetron
- updates to the DPWG guideline for CYP2D6 gefitinib and the addition of the DPWG guideline for UGT1A1 sacituzumab govitecan
Changelog
Features
- data: update data from ClinPGx (af8b4577)
Bug Fixes
- preprocessor: handle unquoted Java version string from Bioconda (#230) (0b1d0fe2). Thanks, @rkmishra3893!
- preprocessor: correct _is_phased() early return and prevent KeyError on duplicate variants (#222) (67e36690). Thanks, @haoyu-haoyu!
- preprocessor: quick fix to not crash due to unordered symbolic structural variants (#225) (76360022)
- preprocessor: fix bug when running pipeline on a directory (#229) (b67ebb0a)
- preprocessor: don't display ambiguity warning if gene is effectively phased (#219) (1767da4e)
- preprocessor: use long form for bcftools -W to support v1.18 (7b075811)
- preprocessor: update versions of htslib/bcftools dependencies (bf2ab5b4)