chain2paf

convert CHAIN format to PAF format

installation

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

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.

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Comments

Optional input FASTA file to write =/X CIGAR operators

chain2paf --input x.chain | head -n 1
S1_12   500     7       414     +       S1_2520 500     95      500     405     407     255     cg:Z:94M1I27M1I284M

chain2paf --input x.chain --fasta input.fa.gz | head -n 1
S1_12   500     7       414     +       S1_2520 500     95      500     403     407     255     cg:Z:94=1I27=1I100=2X182=

opened by AndreaGuarracino 0