v0.2.0

1. Added a module called verdict to statistically classify a called variant into either a germline, somatic, or subclonal somatic variant based on the copy number alterations (CNA) profile and tumor purity estimation. To disable, use --disable_verdict option. Verdict module is based on ASCAT algorithms and appropriate to use with tumor purity estimation lower than 0.8.

v0.1.0

1. Added support for somatic Indel calling. To disable, use --disable_indel_calling. Indels are called only in the BED regions specified by the --calling_indels_only_in_these_regions option. The default regions are (whole genome - GIAB stratification v3.3 all difficult regions + CMRG v1.0 regions).
2. Added --panel_of_normals_require_allele_matching option that takes comma separated booleans to indicate whether to require allele matching for each of the PoNs given in --panel_of_normals. By default, allele matching is enabled when using germline variants sources (e.g., gnomAD, dbSNP) for non-somatic tagging, and is disabled when using panels (e.g., 1000G PoN).
3. Added multiple filters to remove as many spurious calls as possible. Including the use of i. phasing information: how good the alternative alleles are from a single haplotype after phasing (Simpson, 2024); ii. ancestral haplotype support: can an ancestral haplotype be found for reads that contain the alternative allele (Zheng et al., 2023); iii. BQ, MQ of the alternative allele reads; iv. variant position in read: whether the supporting alleles are gathered at the start or end of reads; v. strand bias; vi. realignment effect: for short read, whether both the count of supporting alt alleles and AF decreased after realignment.
4. Added --qual_cutoff_phaseable_region and --qual_cutoff_unphaseable_region to allow different qual cutoffs for tagging (as LowQual) the variants in the phaseable and unphaseable regions. Variants in unphaseable regions are suitable for a higher quality cutoff than those in the phaseable regions.
5. Added tags: i. H to indicate a variant is found in phaseable region; ii. SB showing the p-value of Fisher’s exact test on strand bias.

v0.0.2

1. Added ONT Guppy 5kHz HAC (-p ont_r10_guppy_hac_5khz) and Dorado 4kHz HAC (-p ont_r10_dorado_hac_4khz) models, check here for more details.
2. Added FAU, FCU, FGU, FTU, RAU, RCU, RGU, and RTU tags for the count of forward/reverse strand reads supporting A/C/G/T.
3. Revamped the way how panel of normals (PoNs) are inputted. Population databases are also considered as PoNs, and users can disable default population databases and add multiple other PoNs.
4. Added file and md5 information of the PoNs to the VCF output header.
5. Enabled somatic variant calling in sex chromosomes.
6. Fixed an issue that misses PoNs tagging for low-quality variants.

v0.0.1

Initial release for early access.