What's Changed major edits by @mgaleyuw in https://github.com/millerlaboratory/needLR/pull/12 merged into the main branch needLR is contained in one script and has subcommands that replace separate mode scripts merged VCFs can be used with custom cohorts VCFs can be bgzipped and indexed by needLR query VCFs can be provided as positional arguments, in a text file list, or as a merged VCF custom control VCFs can be used with duo, trio, and with multisample VCFs analysis can be restricted to a subregion (e.g. chrX:12345-23456) annotations can be selected a la carte OMIM modes of inheritance are in a separate column genCC modes of inheritance and support levels are in a separate column additional CPU thread argument can be passed to BCFtools output can be saved in a custom location needLR can run from any working directory when installed through bioconda biocontainer installation possible reference fasta file no longer used. This speeds up Truvari merging awk statements are reworked for increased flexibility and reproducibility added help functions and eror messaging gene indexed annotations reworked position based annotations all use bcftools annotate when possible vcf output header includes all contigs in input vcfs Full Changelog: https://github.com/millerlaboratory/needLR/commits/v4.0 Note that release does not include backend files necessary to run needLR. Please follow installation instructions in the README.