- fairegions: (fai) generate equal length regions from an fai (for parallelization)
- combine_slivar_counts: combine counts from slivar for original call and for compound-hets
- highcov: (bam/cram) find high-coverage regions (~3 minutes per 30X cram)
- meandepth: (bam/cram) quickly calculate meandepth by sampling (~2 seconds)
- samplename: (bam/cram) print sample name from readgroup tag
- setsvalt: (vcf/bcf) set the ALT allele in a manta VCF to left + N + right for paragraph genotyper
- setref: (vcf/bcf) change ref allele from N to the actual allele.
- slivar_split_fam: (vcf/bcf) split joint slivar files by family and inheritance mode
- sum_slivar_counts: sum counts from slivar from same samples split across multiple files/regions
- vcf2bedpe : convert and SV VCF to simple bedpe