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Which is the current standard, ARS-UCD1.2 or ARS-UCD2.0?

Hi all, I was wondering which reference of bovine genome is better to use in a standard SNP calling pipeline, ARS-UCD1.2 or ARS-UCD2.0? I see that 1.2 is more widely used and has better possibility of having annotation etc files in resource bundles, while 2.0 is better in quality but is not as widely used yet. On the UCSC web-site I can't even see which bostau9 version their liftover file has (since 1.2, 1.3, 2.0 are all bostau9, seems like). Is it like T2T vs Hg38 in humans?

Also, NCBI says 1.2 version is contaminated. Is it safe to download it then? Or where is it better to?

cow reference
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updated by GenoMax GenoMax • written by mary.v.volkova • mary.v.volkova

1 answer

In general latest release of any genome is preferred since it represents the "state of the art" of that genome (e.g. that is a reason why it is a major release instead of a point release e.g. 1.2,1.3 etc). That said, people sometimes use the major prior version (n-1) because of resources (mainly deeper annotation) and associated data/publications.

Is it like T2T vs Hg38 in humans?

Not completely but ARS-UCD2.0 contains T2T sequenced Y chromosome (see https://bovinegenome.elsiklab.missouri.edu/history) otherwise it seems to be identical to ARS-UCD1.3.

As for the SNP calling consider this answer: Cattle reference genome ARS-UCD2.0.

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written by GenoMax GenoMax

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