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.