v1.8

Update supported Python version from 3.6 to 3.11.

v1.7

Adjust PEACH to support UGT1A1 calling.
Specifics:

• Ignore gene of variant in VCF and only use gene names from panel JSON.
• Allow multiple calls at the same location if reference allele matches.
  • Needed for UGT1A1 *28/*37.
• Add option to panel JSON to specify variants to ignore.
  • Needed for UGT1A1 *36.
• Stop treating empty variant annotation as unknown variant annotation, but instead indicate as annotation=”NONE”.

v1.6

Changes:

• Make --sample_t_id argument optional.
• Fix crash when PAVE_TI has "Number=." in VCF header.

v1.5

Changes:

• Add support for PAVE annotations.
• Add optional "canonicalTranscript" entry in panel JSON.
  • This entry is required for parsing PAVE annotations, and ignored for SNPEFF annotations.

v1.4

Changes:

• Change formats of output files to essentially being PEACH v1.0 output files with some additional columns, to avoid breaking the expectations from downstream tools based on semantic versioning.

v1.3

Changes:

• Update sciki-allel version to fix pip-install failure.

v1.2

Changes:

• Allow for different chromosome names wrt v37 and v38
  • Includes changes to the panel JSON and the genotype output file.
• Improve clarity and consistency of logging.

v1.1

Changes:

• Add shell script peach for running PEACH.
• Remove VCF filtering step.
  • Remove VCFTools dependency.
  • Remove filtered vcf output file.
• Add experimental support for input VCF's for reference genomes with version v38.
• Change format of arguments to PEACH.
  • Arguments are no longer positional.
  • Remove arguments vcftools, recreate_bed and transcript_tsv, since they are no longer needed.
  • Add optional parameter for experimental v38 VCF support.
• Change format of panel JSON.
  • Change key "url_prescription_info" to "urlPrescriptionInfo" for consistency with other keys.
  • Add "annotationV37" key for reference sequence differences, for support of v38 reference genomes.
• Adjust format of genotype TSV output file.
  • Split "haplotype" column into "haplotype" and "zygosity".
• Add script for running tests.

v1.0

First release of PEACH.

See also https://github.com/hartwigmedical/peach