# Trios

Menu: **[patient] -> [trios]**

A trio is a collection of 3 samples (mother/father/proband) which are frequently analysed together in high throughput sequencing, as they have a number of standard analyses.

## Creating a trio

It is far better to upload a trio within the same [multi-sample VCF](../data/vcf_samples.md). If not, you must first create a cohort containing the 3 samples/

View the VCF or cohort, select exactly 3 samples then click the **[Perform Trio Analysis using template]** button.

![Creating a Trio](../data/images/multi_sample_vcf.png)

The Trio wizard will now open, showing the 3 samples and patient / phenotype info. Assign samples (1 each to mother/father/proband) and check mother or father affected if they also have the disorder.

## Digital karyomapping

By checking a trio's zygosity, it's possible to perform a number of relatedness calculations, see [karyomapping](../analysis/karyomapping.md).

A genome-wide count is automatically performed, and a summary provided on the trio page - this is useful for checking for sample mix-ups. 

## Trio inheritance analysis

An analysis is created using different inheritance models (see below). If either parent is affected it will also use an autosomal dominant inheritance model.

![Trio inheritance analysis](images/trio_analysis.png)

The phenotype at the bottom uses the proband patient phenotypes, and sample gene lists.

### Require Zygosity Calls

By default, the filters are strict and require zygosity calls in all patients - for instance the recessive inheritance model requires a variant to be HOM in proband and HET in both parents.

However that may be overly strict - one parent may have low coverage, with no variants recorded at that locus.

Click on an Trio node to open the editor - unchecking the **require zygosity calls** box is less strict and allow for variants that are missing due to low coverage.

### Compound Het filter

Compount heterozygous means 2 variants in the same gene from different parents.

The C. Het node in the bottom right of the screenshot above is a filter node - ie it has another node connected to the top, while the other inheritance models do not.

This is because you probably don't want every gene with >=2 variants, but rather only >=2 damaging/rare ones. Adjust the filters above the C.Het node to adjust this.

Modify the analysis as per instructions below to filter to all of them.

![](images/all_comp_het.png)