v2.1.0

Changed

• ClinVar version in SnpEff container updated to version 20240307.
• Convert to BAM only when --cnv --use_qdnaseq is selected.
• Update to Clair3 v1.0.6.
• Update Spectre to fix an error when parsing Clair3 VCFs with multiple AFs.
• Support for an input folder of multiple BAM files per sample with --bam (instead of only allowing a single BAM per sample).
• refine_with_sv to be run by chromosome in order to reduce memory footprint.

Fixed

• Force minimap2 to clean up memory more aggressively. Empirically this reduces peak-memory use over the course of execution.
• Handling of input VCF files with --vcf_fn.
• --phased --sv --snp generates a truncated VCF file when # appears in the VCF INFO field
• Some reporting scripts using too much memory.

Removed

• CRAM as supported input format.
• old_ref parameter as providing the reference of an existing CRAM is no longer needed.