Comparing genotypes to a reference genome

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Jan 10, 2022, 3:50:45 PM1/10/22

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Hi Dr. Broman,

In est.map, or for instance in running "imp", can I reference genotypes back to a reference genome instead of to the cross parents?

For example, while several neighboring markers are all fixed for P1's genotype, the calls will show a mix of AA & BB if called from a reference.

Thank you

Annie

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Jan 10, 2022, 4:02:39 PM1/10/22

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No. In R/qtl they need to be relative to the two cross parents.

karl

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