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readme.pregsf90 [2019/07/26 21:57] ignacio [Input files] |
readme.pregsf90 [2019/09/04 17:31] ignacio [Quality Control (QC) for G] |
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<file>OPTION sex_chr n</file> | <file>OPTION sex_chr n</file> | ||
Chromosomes number equal or greater than //n// are not consider autosomes.\\ | Chromosomes number equal or greater than //n// are not consider autosomes.\\ | ||
- | If selected this option, sex chromosomes will not be used for checking parent-progeny Mendelian conflicts and HWE\\ | + | If selected this option, sex chromosomes will not be used for checking parent-progeny Mendelian conflicts, HWE and heritability of gene content\\ |
but they will be included for all remaining processes. **If you want to remove sex chromosomes**, which we do recommend, use ''OPTION excludeCHR''. | but they will be included for all remaining processes. **If you want to remove sex chromosomes**, which we do recommend, use ''OPTION excludeCHR''. | ||
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The test is useful for homogenous populations (breeds) but theory does not hold for crossbred animals. | The test is useful for homogenous populations (breeds) but theory does not hold for crossbred animals. | ||
This test uses explicitly inv(A22) so it is not suitable for very large populations. | This test uses explicitly inv(A22) so it is not suitable for very large populations. | ||
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