Phenotype Association Tools in Galaxy

Creating the parents altered genomes

We are demonstrating finding an recessive disease or trait. So the expectation is that the disease alleles will be heterozygous in the parents (carriers), and homozygous in affected children. Unaffected children are expected to be either the healthy allele or heterozygous like the parents.

To add the disease alleles to the genome we will concatenate the two datasets, first the disease alleles then the genome. This way the disease alleles will remain at the top and visible in the history panel after any filtering that does not affect the order within the dataset. In the section Text Manipulation, click on Concatenate datasets (red arrow). Select the HetVars (heterozygous variants), then click the Add new Dataset so you can add the mother (red arrows). Then click Execute (green arrow).

Repeat this step this time selecting the father for Dataset 1.

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