v1.16.0

1.16.0 (2026-03-17)

Features

• ALT as somatic sample name and ignore genotype for somatic samples (#165) (37e41f7)

Bug Fixes

• remove vatools env from autobump action to enable autobump (#159) (7195fd5)

Performance Improvements

• autobump snakemake wrappers (#164) (d27fec0)

v1.15.0

1.15.0 (2026-02-05)

Features

• VEP annotation with REVEL, Sift and PolyPhen Scores to fp/fn vcfs (#154) (d2512d0)

Bug Fixes

• change SEQC2 SNV truth to enable VAF comparison for WGS (#157) (925a157)

Performance Improvements

• autobump snakemake wrappers (#155) (bfa37e2)
• bump snakemake wrappers to v8.0.2 (#150) (0647f12)

v1.14.1

1.14.1 (2025-11-14)

Bug Fixes

• avoid creation of vcfs for all callsets for each benchmark (#149) (2de769e)

Performance Improvements

• bump snakemake wrappers to v7.6.1 (#145) (8768c74)
• bump snakemake wrappers to v7.8.1 (#147) (7181d47)

v1.14.0

1.14.0 (2025-10-01)

Features

• add conda to dependabot (#144) (3ad3652)
• add fp-fn-filtering and write to vcf (#137) (95642c1)
• add vaf column to fp/fn tables (#142) (b0a9dd4)
• sort vcfs with shared and unique fp and fn (#143) (c2aaad2)

Performance Improvements

• update tools in conda environments and snakemake wrappers to 7.2.0 (#141) (b645cb6)

dna-seq-benchmark v1.13.0

1.13.0 (2025-08-01)

Features

• add number of expected variants to report and improve the views (#130) (4ada0c1)

Bug Fixes

• link to snakemake workflow catalog (#129) (1c49f2f)
• use buffered and script based get-reads implementation (#126) (b9d4360)

Performance Improvements

• add bot to automatically update github actions monthly (#134) (e1ac2d5)
• update tools in conda environments (#132) (6d2dbc1)
• update snakemake wrappers to 7.0.0 (#131) (d7d9f0e)

dna-seq-benchmark v1.12.2

Bug Fixes

• add dirs with results to rule all (#120) (4dfdf6d)

dna-seq-benchmark v1.12.1

Bug Fixes

• add .get() for optional values in config instead of dict access (#118) (94d9294)

dna-seq-benchmark v1.12.0

Features

• Add heatmap coloring for coverage stratification in fp fn report, hide class label. (#112) (e0d3ea9)
• automate picking of rename file based on reference genome used for calling + setup for more than 2 reference genomes (#113) (2bbb9ae)
• Report FP / FN negative variants in single table (#107) (0464700)
• add rule merge_callsets for snv/indel callsets (#115) (7e5fdde)

Bug Fixes

• catch when FORMAT field is present in truth (#114) (0e8e4be)
• change vaf_field to dict (#110) (e78abbb)
• fix missing index as input for restrict_to_reference_contigs (#102) (c55c503)
• link to truth vcf for na12878-somatic (#116) (724ce2d)

Performance Improvements

• update datavzrd wrapper (#104) (db68793)

dna-seq-benchmark v1.11.7

Bug Fixes

• Only append labels in first iteration of storage loop; calculate chi2 only on non empty feature matrix. (#96) (20a469a)
• restrict calls to reference contigs (#101) (0413580)

dna-seq-benchmark v1.11.6

Bug Fixes

• hide sort_index in results table (#94) (bb72674)