Does what it says: ulitka handles all stages of genomic coordinates liftover from alignments of anchors to making/manipulating chain files and modifying coordinates in VCF and BED files. No sophisticated indel handling, thus only usable for coordinate conversion and SNP liftover. Sometimes that's the only thing needed, right?

If no premade chain file is available, ulitka can make it. It takes knowing where orthologous loci (anchors) are found in two genomes. Then, chain files describing the coordinate conversion are made from FASTA alignments of these regions.

It comes with convenient chain file manipulation commands. Specifically, chains can be "stretched out" into a tabixable one-chain-one-line lchain format and "reversed" by swapping reference and query genomes (effectively enabling tabix queries across both coordinate systems).

Prerequisites are having the following programs in $PATH environmental variable:

• gawk
• tabix
• bgzip
• GNU parallel (to enable parallel execution in ulitka easy)

ulitka itself is zero-install, being entirely written in GNU AWK. Just clone the repo and make ulitka executable:

git clone https://github.com/taprs/ulitka.git
chmod +x ulitka/ulitka

ulitka easy     -- full VCF liftover workflow, optionally parallelized (lift + header) 
ulitka lift     -- lift over VCF file using a chain file
ulitka header   -- update VCF header using a new FASTA file 
ulitka fa2chain -- make a chain file from a FASTA alignment, new ref 1st seq 
ulitka lchain   -- convert chain files to/from indexable lchain files 
ulitka conv     -- convert genomic coordinates (BED or chr:start-end) using chain files 
ulitka rev      -- swap target and query genomes in chain files 
ulitka faidx    -- reimplemented faidx indexing & querying of FASTA files

# Make alignment: put at least two anchor sequences into a FASTA file, new (query) genome first
# Coordinates and orientation are detected from standard faidx naming
ulitka faidx new.fa chrA:1-10 > aln.fa
ulitka faidx --reverse-complement old.fa chrB:11-20 >> aln.fa

# Align with your favorite tool, e.g. mafft aln.fa > aln_fin.fa

# Make the chain file from any number of alignments
ulitka fa2chain -1 old.fa -2 new.fa -f aln_fin.fa > aln.chain

# Lift over VCF, modify header to contain correct ##contig definitions
ulitka easy -f new.fa -c aln.chain -v file.vcf.gz | bgzip > file_liftover.vcf.gz