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Changelog

0.25.0 (2024-06-16)

  • Add 26 new genes: ACYP2, ADRA2A, ADRB2, ANKK1, APOE, ATM, BCHE, BDNF, DBH, DRD2, F2, GRIK1, GRIK4, GRIN2B, HTR1A, HTR2A, IFNL4, ITGB3, ITPA, OPRK1, OPRM1, RARG, SLC6A4, SLC28A3, SLC47A2, UGT1A6.

0.24.0 (2024-03-31)

  • Change G6PD haplotype name from *MALE to MALE, as the gene does not utilize star allele nomenclature.
  • Update G6PD haplotype nomenclature in accordance with the latest CPIC version (2024-01-07).
  • :issue:`119`: Add G6PD phenotype data in accordance with the latest CPIC version (2024-01-07).
  • Update CYP4F2 haplotype nomenclature in accordance with the latest PharmVar version (2024-01-27).

0.23.0 (2023-12-24)

  • :issue:`115`: Add new genes COMT and MTHFR (thanks @nbiesot).
  • :issue:`117`: Fix major bug in :meth:`api.utils.estimate_phase_beagle` method. The bug was introduced in version 0.22.0 (:issue:`113`) and carries significant implications, especially if the user's input VCF contains sample names that overlap with the reference panel or if there are differences in chromosome annotation compared to the reference panel (e.g. 'chr22' vs. '22').

0.22.0 (2023-12-11)

0.21.0 (2023-08-25)

0.20.0 (2023-01-12)

  • :issue:`73`: Fix bug in :command:`run-ngs-pipeline` command where empty VCF (i.e. no variants were found in the target gene) was causing error when plotting allele fraction. From now on, a warning will be produced telling users to specify --do-not-plot-allele-fraction to suppress this warning.
  • :issue:`78`: Fix bug in :command:`compute-copy-number` command where it threw an error "Different sample sets found" when the sample name consists of only numbers.

0.19.0 (2022-09-13)

0.18.0 (2022-08-12)

0.17.0 (2022-07-12)

0.16.0 (2022-06-08)

0.15.0 (2022-05-03)

  • Add new optional arguments --genes and --exclude to :command:`prepare-depth-of-coverage` command.
  • Add new command :command:`slice-bam`.
  • Add new command :command:`print-data`.
  • Fix typo "statistcs" to "statistics" throughout the package.
  • Update :meth:`sdk.utils.simulate_copy_number` method to automatically handle duplicate sample names.
  • Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, UGT2B17.
  • Add new CNV calls for CYP2A6: Deletion2Hom, Hybrid5, Hybrid6, PseudogeneDeletion.
  • Add new CNV call for CYP2D6: Tandem2F.
  • Add new CNV call for GSTM1: Normal,Deletion2.
  • Add new CNV call for SULT1A1: Unknown1.
  • Add new CNV call for UGT2B17: Deletion,PartialDeletion3.

0.14.0 (2022-04-03)

  • :issue:`49`: Add new gene ABCG2.
  • :issue:`50`: Improve algorithm for whole gene duplication detection. This minor update will handle some rare edge cases.
  • :issue:`53`: Update CYP2B6*17 variants to have synonyms. Update :meth:`api.core.get_variant_synonyms` and :meth:`api.utils.predict_alleles` methods to allow mapping of single variant to multiple synonyms.
  • :issue:`54`: Add new command :command:`create-input-vcf`.
  • Fix minor error in gene-table.csv. Two control genes EGFR and VDR incorrectly had TRUE for Variants column. They were changed to FALSE.
  • Change the three paralogs in gene-table.csv (CYP2A7, CYP2B7, and CYP2D7) to have FALSE for SV column.
  • Add new optional arguments to :command:`create-regions-bed` command: --target-genes, --var-genes, --genes, --exclude.
  • Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, UGT2B17.
  • Add new CNV calls for CYP2A6: Hybrid2Hom, Hybrid4, Tandem.
  • Add new CNV calls for CYP2D6: Tandem4, PseudogeneDownstreamDel, Unknown2.
  • Add a new CNV call for CYP2E1: Multiplication2.
  • Add new CNV calls for GSTM1: PartialDuplication and DeletionHet,Deletion2.
  • Add a new CNV call for SLC22A2: PartialDuplication.
  • Add a new CNV call for SULT1A1: DeletionHom.
  • Add new CNV calls for UGT2B15: Deletion2, Duplication, PartialDuplication.
  • Add a new CNV call for UGT2B17: Normal,PartialDeletion3.

0.13.0 (2022-03-01)

0.12.0 (2022-01-29)

  • Update :command:`run-ngs-pipeline` command to allow users to provide a custom CNV caller.
  • Update :meth:`api.core.predict_phenotype` method to not raise an error when a given star allele does not exist in the allele table. From now on, the method will output a warning about it but still produce an Indeterminate call.
  • Fix minor bug with --samples argument in commands :command:`plot-bam-copy-number`, :command:`plot-bam-read-depth`, :command:`plot-vcf-allele-fraction`, and :command:`plot-vcf-read-depth`.
  • Update :meth:`sdk.utils.add_cn_samples` method to accept a list of samples in addition to a file.
  • Add new argument --fontsize to :command:`plot-bam-read-depth` command.
  • Fix minor bug in :command:`plot-bam-read-depth` command.
  • Moved 1KGP reference haplotype panels and CNV callers to the pypgx-bundle repository (only those files were moved; other files such as allele-table.csv and variant-table.csv are intact). From now on, the user needs to clone the pypgx-bundle repository with matching PyPGx version to their home directory in order for PyPGx to correctly access the moved files. This is undoubtedly annoying, but absolutely necessary for portability reasons because PyPGx has been growing exponentially in file size due to the increasing number of genes supported and their CNV complexity, to the point where it now exceeds upload size limit for PyPI (100 Mb). After removal of those files, the size of PyPGx has reduced from >100 Mb to <1 Mb.
  • Add CNV caller for G6PD (mostly for sex determination since it's located on X chromosome).
  • Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SULT1A1, UGT2B15, and UGT2B17.
  • Add new CNV calls for CYP2A6: Duplication2, Duplication3, Deletion2Het, Deletion3Het, PseudogeneDuplication, Hybrid2, Hybrid3. Additionally, some CNV calls have been renamed: Hybrid → Hybrid1; Duplication → Duplication1; DeletionHet → Deletion1Het; DeletionHom → Deletion1Hom.
  • Add a new CNV call for CYP2B6: Duplication.
  • Add new CNV calls for CYP2D6: Unknown1, Tandem1B, Multiplication. Additionally, some CNV calls have been renamed: Tandem1 → Tandem1A; DeletionHet,Tandem1 → DeletionHet,Tandem1A; Duplication,Tandem1 → Duplication,Tandem1A.
  • Add a new CNV call for CYP2E1: Duplication2. Additionally, a CNV call have been renamed: Duplication → Duplication1.
  • Add new CNV calls for GSTM1: UpstreamDeletionHet and DeletionHet,UpstreamDeletionHet.
  • Add a new CNV call for UGT2B15: PartialDeletion2. Additionally, a CNV call have been renamed: PartialDeletion → PartialDeletion1.
  • Add a new CNV call for UGT2B17: PartialDeletionHet.

0.11.0 (2022-01-01)

  • Fix minor bug in :command:`compute-copy-number` command.
  • Update :command:`plot-cn-af` command to check input files more rigorously.
  • Add new method :meth:`sdk.utils.add_cn_samples`.
  • Update :command:`compare-genotypes` command to output CNV comparisonw results as well.
  • Update :command:`estimate-phase-beagle` command. From now on, the 'chr' prefix in contig names (e.g. 'chr1' vs. '1') will be automatically added or removed as necessary to match the reference VCF’s contig names.
  • Add index files for 1KGP reference haplotype panels.
  • Add new argument --panel to :command:`run-chip-pipeline` command.
  • Remove 1KGP reference haplotype panels for GSTT1 and UGT2B17 because these genes only have star alleles defined with SV.
  • Change 1KGP reference haplotype panels for GRCh38. Previously, PyPGx was using the panels from Lowy-Gallego et al., 2019 where the authors had aligned sequence reads against the full GRCh38 reference, including ALT contigs, decoy, and EBV/IMGT/HLA sequences. This resulted in poor phasing/imputation performance for highly polymorphic PGx genes (e.g. CYP2D6) presumably because the panels were missing haplotype information for lots of SNVs/indels as sequence reads with those variants were mapped to ALT contigs; however, the panels were still the best option at the time (definitely better than lifting over GRCh37 panels). Fortunately, Byrska-Bishop et al., 2021 from New York Genome Center has recently published a new set of GRCh38 panels which apparently has less of this problem despite still having sequence reads aligned in the presence of ALT contigs, etc. When empirically tested, these panels showed a significant increase in phasing/imputation performance. Therefore, from now on, PyPGx will use these panels for GRCh38 data.
  • Update GRCh38 variant information for following alleles: CYP2D6*35, CYP2D6*45, CYP2D6*46.
  • Update gene region for SLC22A2 to match GRCh37 and GRCh38.
  • Add CNV caller for CYP4F2 and SULT1A1.
  • Improve CNV caller for CYP2A6, CYP2D6, and SLC22A2.
  • Add a new CNV call for CYP2D6: Tandem3.

0.10.1 (2021-12-20)

  • Fix major bug where CNV callers are not packaged properly.

0.10.0 (2021-12-19)

0.9.0 (2021-12-05)

0.8.0 (2021-11-20)

0.7.0 (2021-10-23)

0.6.0 (2021-10-09)

0.5.0 (2021-10-02)

0.4.1 (2021-09-21)

  • Initial release.