Liftover nonmodel VCF
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8 months ago

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...

chain file liftover satsuma ucsc • 302 views
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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.

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