Liftover nonmodel VCF

Question

[raf.marcondes]

Hi all, I have a FASTA genome assembly and a VCF for my (nonmodel) study species. Now I want to liftover the VCF to the Zebra Finch genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_003957565.1). I've found Picard LiftOver GATK and CrossMap, but both require a UCSC chain file, which apparently can only be generated between assemblies of model organisms available at UCSC. Any thoughts on how to generate a chain file for my study speciesXzebra finch? Or lift over the VCF some other way? I've played around with Satsuma2 a little, but doesn't look like it can generate a UCSC chain file...

[Ram]

liftOver README clearly mentions that it is not meant for between-species operations. One option would be to run alignment + variant calling against the zebra fish genome from scratch.

Answer 1

[Luis Nassar]

Hello,

If you contact the Genome Browser ([e-mail]) we can usually create liftOver files between any assembly so long as it's on genbank (GCF_), such as the Zebra Finch (https://genome.ucsc.edu/h/GCF_003957565.2).

However, in cases like yours where one of them is a local FASTA genome that's not possible as our pipeline is heavily reliant on the genbank process. We offer some some guidance on how to replicate this process for different species (http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl) but that can be a can of worms.

If you decide to try to tackle that process and need additional assistance, or would like a liftOver between GCF_ assemblies, our public help desk can always be reached at [e-mail]. You may also send questions to [e-mail] if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.

Answer 2

[Philipp Bayer]

If Luis' solution fails, you could get LiftOff to work with some creativity. It normally takes only gff3 files, you'd have to make one based on your VCF and the SNP's flanking region. See this older issue https://github.com/agshumate/Liftoff/issues/11