chain2paf

convert CHAIN format to PAF format

citation

installation

chain2paf is built with rust, and so we install using cargo:

git clone https://github.com/AndreaGuarracino/chain2paf
cd chain2paf
cargo install --force --path .

usage

With alignments in data/hg18ToHg19.over.chain, we would convert it into a PAF format file using this call:

chain2paf -i data/hg18ToHg19.over.chain > hg18ToHg19.over.chain.paf

If full CIGAR strings (with =/X operators) are required, we can specify two FASTA files (uncompressed or bgzipped), the 1-st for the targets and the 2-nd for the queries. For example, if the sequences of the human genome versions hg18 and hg19 are available in the hg18.fa.gz and hg19.fa.gz files, you can execute

chain2paf -i data/hg18ToHg19.over.chain -f hg18.fa.gz hg19.fa.gz > hg18ToHg19.over.chain.paf

If the CHAIN file is the result of a pairwise alignment, you can specify the same FASTA file for both targets and queries:

chain2paf -i input.chain -f input.fa.gz input.fa.gz > input.chain.paf

info

chain2paf performs the reverse operation of paf2chain.