millerlaboratory/needLR: needLR v4.0

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.