HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Trio analysis producing incorrect results from 'unknown zygosity' tracks in Genomics Workbench 6.5 and previous

3.18. Trio analysis producing incorrect results from 'unknown zygosity' tracks in Genomics Workbench 6.5 and previous

This issue relates to only those cases where the trio analysis was run using variant tracks containing variants with 'unknown' zygosity. This would apply to e.g. a scenario with more than one affected child and where the 'child' input track for the trio analysis consisted of a 'common' sibling variant track created using the tools 'Compare Sample Variants' and 'Compare Variants Within Groups'. With these tools, if a variant is found in more than one offspring but with different zygosity the zygosity reported in the output track will be 'unknown'.

This issue does not apply to a regular trio analysis with a basic '1 child-mother-father' variant set.

The implications:

The trio analysis tools requires the zygosity information to find out if a variant is de novo or not, and if a variant looks suspicious.

In Genomics Workbench 6.5 and earlier versions the trio analysis would run despite input variants were listed as having unknown zygosity. This would have given rise to potentially incorrect results. Therefore, we strongly recommend that all affected trio analysis are re-run in Genomics Workbench 6.5.1

From Genomics Workbench 6.5.1 trio analysis will no longer run when input tracks contain 'unknown' zygosity variants. To run a trio analysis with more than offspring involved you will need to consider one of the following approaches:

1. Use alternate filtering tool to find common variants (only zygosity of sib 1 will be used)

Use the following filter to find the offspring common variants: Toolbox|Resequencing Analysis|Annotate and Filter Variants|Filter against Known Variants


Please note that with this tool the zygosity in the output 'common' track with be identical to offspring 1 (the filtered track/first input). You will want to consider the implications for variants where the zygosity is not identical between offspring.

2. Running one trio analysis per sibling and merging the results

Run one trio analysis for each offspring.

Filter the trio analysis outputs using 'Filter Variants Within Groups' to find the common variants.

Knowledge Tags
Trio  / 

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