Add optional parameters for SV/SNV filtering and calling configuration

[ktruve]

Description of feature

We have implemented the following optional parameters in our fork and would like to propose them for upstream inclusion:

Parameter	Default	Description
filter_expansionhunter_htt	false	Filter HTT (Huntington) records from ExpansionHunter output
filter_sv_to_manta	false	Exclude TIDDIT from SVDB_MERGE keeping only Manta SVs
skip_vep_sv	false	Skip VEP annotation of SVs; SVDB_QUERY still runs
sv_size_threshold	null	Filter SVs larger than this value in bp (e.g. 1000000); null = no size filter
sv_freq_filter_expression	null	bcftools -e expression for SV frequency filtering (e.g. INFO/SWEFRQ >= 0.02)
manta_call_regions	null	BED.gz file restricting Manta to specific regions; null = whole genome (including decoy)
ml_prob_threshold	null	ML_PROB threshold for Sentieon DNAscope; null = use Sentieon's own MLrejected flag
normalize_multiallelics	false	If true adds --multiallelics -both to bcftools norm; false avoids ~4% indel precision loss

All parameters are optional with sensible defaults that preserve existing pipeline behaviour.