ntRoot v1.1.6

• Release v1.1.6
• Added changes to be compatible with ntEdit v2.1.1+, where the reads prefix (--reads) can now be a relative or absolute path to the reads directory
  • Backwards compatible - if no path specified, it will search the current working directory for input files as before

ntRoot v1.1.5

• Release v1.1.5
• Fix for --custom_vcf mode
  • Allow variant (non-header) lines in the input VCF to have internal # characters

ntRoot v1.1.4

• Release v1.1.4
• Refactoring single-character parameters of ntroot_run_pipeline.smk
  • Newer snakemake versions fail to properly parse single-character config keys
  • Use multi-character parameter strings to ensure compatibility

ntRoot v1.1.3

• Release v1.1.3
• Added flexibility for parsing input VCFs when using --custom_vcf
  • Accepts 8-10 columns, auto-detects for parsing bedtools intersect file
    • Previously, required 10 columns (as were present in all VCFs tested), but it is valid to have as few as 8 (as there are 8 required columns as per VCF specifications)
  • If there are more than 10 columns, this would indicate a multi-sample VCF, which doesn't make a lot of sense for using ntRoot to evaluate an individual's ancestry - in this case, an informative error message is printed

ntRoot v1.1.2

• Release v1.1.2
• Added an "Unknown" category to ancestry predictions
  • For cases where a given genomic tile has ambiguous ancestry due to multiple populations having an identical highest score

ntRoot v1.1.1

• Release v1.1.1
• Fixes to workflow so --lai mode is compatible with gzipped reference fasta files
• Mention name of tile resolution output file in ntRootAncestryPredictor.pl in --lai mode

ntRoot v1.1.0

• Release v1.1.0
• Added feature to allow for inferring ancestry from a provided VCF
  • When --custom_vcf is specified, ntRoot will use this VCF for inferring ancestry instead of running ntEdit
  • When using an ntEdit VCF file with a new -l variant call set, use --strip_info to ensure that there are no collisions between existing cross-referenced allele assignments in the ntEdit VCF and new cross-referenced alleles
• Updated ancestry inference script to allow for comma-separated allele frequencies when alt alleles exist
• Documentation updates

ntRoot v1.0.1

• Release v1.0.1
• Make ntEdit2 a dependency instead of using it as a submodule
  • The meson build system was removed due to there no longer being any compiled components of ntRoot
• Documentation updates

ntRoot v1.0.0

Initial release of ntRoot: Ancestry inference from genomic data