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@github-actions github-actions released this 05 Nov 05:14
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v0.6.6
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v0.6.6: bundle WGSExtract CLI v0.6.6

WGSExtract CLI v0.6.6

New

  • Nanopore (ONT) support: ONT reads are detected and their MM/ML methylation tags kept through alignment. DeepVariant uses the ONT_R104 model for R10.4.1 reads, Sniffles calls structural variants by default, and Clair3 is an optional small-variant caller (vcf clair3).
  • Methylation pileup: CpG methylation from MM/ML tags with modkit.
  • Y-DNA: native Yleaf-derived haplogroup analysis with verified data assets, and Y-STR genealogy marker panels from WGS (lineage y-str).
  • Variant tables: vcf table writes a queryable one-row-per-variant TSV and SQLite file. Table outputs also accept --format tsv|parquet.
  • Confidence labels: rare and clinical variant calls are labelled with depth-aware confidence.
  • Result manifests: commands can describe their outputs as JSON (--json), with consistent exit codes.
  • Sample workspace: sample facts are recorded once and can be overridden by the user.
  • Typed Python API (phase 1).
  • Easier help: commands are grouped into tiers, typos in options get suggestions, and there are --help-all, help topics, typed help JSON and next-step hints. Global options are now accepted after the subcommand too.
  • report-issue: opens a redacted, pre-filled GitHub bug report.
  • Microarray: info chip detects vendor chip revisions, and --quirks vendor reproduces known vendor reverse-strand reports.
  • Native Linux ARM64: DeepVariant 1.10 runs natively on the CPU for WGS. It uses a locally built image.
  • Recognized inputs: Element AVITI read names, MyHeritage Ultima read names, and the hs38d1c/hs38d1t references.
  • QC: warns about low-coverage or heavily imputed genotype inputs.
  • MultiQC: metrics output, plus docs on handing results to other pipelines. There is also a new hardware and acceleration guide.

Fixes

  • DeepVariant: CRAM 3.1 input is automatically converted to a temporary CRAM 3.0 copy, and the whole-genome postprocess step's RAM is estimated and capped.
  • Realign streams paired reads through collate at whole-genome scale, and refuses single-end reads before extracting pairs.
  • info infers sex when chrX or chrY is missing.
  • Nested --genome IDs inside genome_library are accepted.
  • Slow tool version probes are retried, and successful ones are cached.
  • Faster: coordinate projections and catalogues for microarray are cached, GERP/PhyloP scores are read in bounded windows, consensus queries only records inside the masked regions, and both depth binning and CRAM record counting are quicker.

Full changelog: WGSExtract/wgsextract-cli@v0.6.5...v0.6.6

Full CLI release: https://github.com/theontho/wgsextract-cli/releases/tag/v0.6.6

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