macOS aligners macos-aligners-6

Optional Apple Silicon (macOS 13+, arm64) rebuilds of BWA 0.7.19 and BWA-MEM2 2.3. Not used by the wgsextract CLI yet.
Both align on the CPU by default. Their EXPERIMENTAL --metal flags offload seeding (wgse-bwa) or seed extension (wgse-bwa-mem2) to the GPU.
Built from native/ at a821944 by https://github.com/WGSExtract/wgsextract-cli/actions/runs/42319713587.
See native/README.md for usage, benchmarks and licences.

Package	SHA-256
wgse-bwa-0.6.0-macos-arm64.tar.gz	fe802f2f2953e935cb157c96cc8452e02992694de6a8c8058f28d00057772f83
wgse-bwa-mem2-0.1.0-macos-arm64.tar.gz	4eee075f34302085c08f6ba70fa1f6ba9d4f6ad7687be16f082c8e2847f36b3c

Report gene lists v3

Gene lists for wgsextract report --gene-list (#397), with each gene's mode of inheritance for carrier status (#398). acmg_sf_v3.3.tsv (84 genes; Lee K et al. Genet Med 2025;27(8):101454, PMID 40568962) and acmg_sf_v3.2.tsv (81 genes; Miller DT et al. Genet Med 2023;25(8):100866, PMID 37347242). Gene symbols, categories and inheritance (AD, AR, SD semidominant, XL) are facts from each paper's Table 1; notes paraphrase its inheritance column and footnotes. Gene spans are unchanged from v2: built by scripts/build_report_gene_lists.py, each gene's hg38 span is its MANE Select transcript in NCBI RefSeq annotation release GCF_000001405.40-RS_2025_08 (GRCh38.p14), its hg19 span its RefSeq Select transcript in release 105.20220307 (GRCh37.p13), MD5-verified against NCBI's md5checksums.txt; APC also covers promoter 1B (NM_001127511). Adds the inheritance column to v2. NCBI RefSeq annotation and UCSC refGene (the cross-check, limit and reviewed exceptions recorded in build_info.json) are public data without use restrictions. SHA256SUMS lists every asset's SHA-256; the app pins them in src/wgsextract_cli/assets/report/gene_lists.json. This is a data-only release, not an application update.

Report gene lists v2

Gene lists for wgsextract report --gene-list (#397). acmg_sf_v3.3.tsv (84 genes; Lee K et al. Genet Med 2025;27(8):101454, PMID 40568962) and acmg_sf_v3.2.tsv (81 genes; Miller DT et al. Genet Med 2023;25(8):100866, PMID 37347242). Gene symbols and categories are facts from each paper's Table 1; notes paraphrase its inheritance column and footnotes. Built by scripts/build_report_gene_lists.py: each gene's hg38 span is its MANE Select transcript in NCBI RefSeq annotation release GCF_000001405.40-RS_2025_08 (GRCh38.p14), its hg19 span its RefSeq Select transcript in release 105.20220307 (GRCh37.p13), MD5-verified against NCBI's md5checksums.txt; APC also covers promoter 1B (NM_001127511). Supersedes v1, whose merged-transcript hg38 spans reached neighbouring genes (MSH2 into KCNK12, BRCA1 into NBR2). NCBI RefSeq annotation and UCSC refGene (the cross-check, limit and reviewed exceptions recorded in build_info.json) are public data without use restrictions. SHA256SUMS lists every asset's SHA-256; the app pins them in src/wgsextract_cli/assets/report/gene_lists.json. This is a data-only release, not an application update.

macOS aligners macos-aligners-5

Optional Apple Silicon (macOS 13+, arm64) rebuilds of BWA 0.7.19 and BWA-MEM2 2.3. Not used by the wgsextract CLI yet.
Both align on the CPU by default. Their EXPERIMENTAL --metal flags offload seeding (wgse-bwa) or seed extension (wgse-bwa-mem2) to the GPU.
Built from native/ at 05e749b by https://github.com/WGSExtract/wgsextract-cli/actions/runs/42206837623.
See native/README.md for usage, benchmarks and licences.

Package	SHA-256
wgse-bwa-0.5.0-macos-arm64.tar.gz	867f96b9fc40b3ac8d27ddf7f9c33d387855ecde6ba9a45422b4c5a58d63f058
wgse-bwa-mem2-0.1.0-macos-arm64.tar.gz	0cbf5c4502a51e206824b5982fbd655b0940193a7680cb2bb76742964a08beea

macOS aligners macos-aligners-4

Optional Apple Silicon (macOS 13+, arm64) rebuilds of BWA 0.7.19 and BWA-MEM2 2.3. Not used by the wgsextract CLI yet.
Both align on the CPU by default. Their EXPERIMENTAL --metal flags offload seeding (wgse-bwa) or seed extension (wgse-bwa-mem2) to the GPU.
Built from native/ at ec8e73c by https://github.com/WGSExtract/wgsextract-cli/actions/runs/42178246935.
See native/README.md for usage, benchmarks and licences.

Package	SHA-256
wgse-bwa-0.4.0-macos-arm64.tar.gz	67e41c31587e90739d149f98ad949607f87d4724905176ab74e401354b569302
wgse-bwa-mem2-0.1.0-macos-arm64.tar.gz	bead14b5fef2620e8eb889810c116e7615c1de86a8f85ccb767c5cd91c1289f5

macOS aligners macos-aligners-3

Optional Apple Silicon (macOS 13+, arm64) rebuilds of BWA 0.7.19 and BWA-MEM2 2.3. Not used by the wgsextract CLI yet.
Both align on the CPU by default. Their EXPERIMENTAL --metal flags offload seeding (wgse-bwa) or seed extension (wgse-bwa-mem2) to the GPU.
Built from native/ at 98c4d6e by https://github.com/WGSExtract/wgsextract-cli/actions/runs/42139962969.
See native/README.md for usage, benchmarks and licences.

Package	SHA-256
wgse-bwa-0.3.0-macos-arm64.tar.gz	af4a23ee5531f89044362e46f157f47f416bc000c06659fc312be2dbf396ba38
wgse-bwa-mem2-0.1.0-macos-arm64.tar.gz	1558e19b13310cb89f46c980661e6e90c9ab0d792bc14149ed63c84e42129373

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: v0.6.5...v0.6.6

YFull YTree 14.06.0 tree pack (native Y-DNA)

Versioned YFull tree pack for lineage y-haplogroup --tree yfull (#359). Built reproducibly by scripts/build_yfull_tree.py from YFull YTree 14.06.0 (YFullTeam/YTree commit bdc9bb4d8db72abc7658362f258dbc2a63e34789, ytree/tree_14.06.0.zip, 2026-09-22) and a YBrowse snps_hg38.csv snapshot retrieved 2026-11-05; hg19 and T2T positions lifted with Yleaf v4.1.6's UCSC chains. Contains Yleaf's tree.json and hg19/hg38/T2T new_positions(_ancient).txt marker tables; build_info.json records every input's SHA-256 and the marker counts. The YFull tree is licensed CC-BY-4.0 (LICENSE-YTree.md): YFull, https://www.yfull.com, https://github.com/YFullTeam/YTree. Marker positions are adapted from YBrowse (https://ybrowse.org), CC-BY-SA Thomas Krahn YSEQ (2022), and shared under the same terms (NOTICE-YBrowse.md); the exact YBrowse snapshot used is attached as ybrowse-snps_hg38-2026-11-05.csv.gz. build_info.json also records each reference's chrY name, length, MD5 and SHA-256. This is a data-only release, not an application update.

ONT HG002 R10.4.1 validation data (v1)

Validation data for Oxford Nanopore R10.4.1 support (#299). These are slices of ONT's public GIAB HG002 alignment, used to check wgsextract against the GIAB truth sets. They are not needed to run the program.

Source: s3://ont-open-data/giab_2023.05/analysis/hg002/sup/PAO83395.pass.cram. Oxford Nanopore Technologies open data, CC BY 4.0. Basecalled with dna_r10.4.1_e8.2_400bps_sup@v4.0.0 (5mCG_5hmCG), aligned to GRCh38 no-alt (hs38) with minimap2.

Asset	Contents
hg002_ont_r1041_chr20_10-15Mb.cram	chr20:10,000,000-15,000,000, about 54x
hg002_ont_r1041_chr20_part1.cram	chr20 reads starting at or before 32,000,000
hg002_ont_r1041_chr20_part2.cram	chr20 reads starting after 32,000,000

GitHub limits each asset to 2 GiB, so whole chr20 comes in two parts. samtools cat part1.cram part2.cram joins them. All the CRAMs need the hs38 FASTA to decode.

SHA-256 sums, sizes and the GIAB truth URLs are in docs/data/ont_hg002_manifest.json. python scripts/ont_hg002_data.py fetch downloads and verifies them. Results are in docs/ont.md.

macOS aligners macos-aligners-2

Optional Apple Silicon (macOS 13+, arm64) rebuilds of BWA 0.7.19 and BWA-MEM2 2.3. Not used by the wgsextract CLI yet.
Both align on the CPU by default. Their EXPERIMENTAL --metal flags offload seeding (wgse-bwa) or seed extension (wgse-bwa-mem2) to the GPU.
Built from native/ at f3b780d by https://github.com/WGSExtract/wgsextract-cli/actions/runs/42106057044.
See native/README.md for usage, benchmarks and licences.

Package	SHA-256
wgse-bwa-0.2.0-macos-arm64.tar.gz	f2357280a83622124ed118b96f669b85c71b3f5d79c40b6e27caa17ab3723aeb
wgse-bwa-mem2-0.1.0-macos-arm64.tar.gz	f06ac3235979a5451c78bbe5c6d6d17d9ca229d1c95e193a12888ebd2519cd34