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#909 - improve documentation
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davmlaw committed Oct 4, 2023
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7 changes: 5 additions & 2 deletions analysis/nodes.md
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Expand Up @@ -47,7 +47,8 @@ By default cohorts are filtered using only the simple zygosity method: Het or Ho

"Any Zygosity" = Hom/Het/Ref (ie anything other than 'unknown'). Unknown zygosity is when there is no coverage over the variant for this sample.

These counts are applied simultaneously, so be careful the ref/het/hom alt minimums don't add up to more than the number of samples in the cohort.
These counts are applied together in an AND-like manner. Warning: It's possible to set ref/het/hom alt minimums that add up to more than the number of samples in the cohort, which will always be false, and so exclude all variants.

### Classifications

![](images/nodes/node_classifications.png "Classifications")
Expand Down Expand Up @@ -311,7 +312,9 @@ Most genetic diseases are rare (eg 1 in 10,000 people) so we know the disease-ca

This node filters variants by population frequency in public databases ([gnomAD](https://gnomad.broadinstitute.org/)/[TopMed](https://topmed.nhlbi.nih.gov/)/[1KG](https://www.internationalgenome.org/1000-genomes-summary/)/[UK10K](https://www.uk10k.org/)) or [internal frequency in this database](../data/zygosity_counts.md).

Click "Pick individual gnomAD populations" to expand the selection to sub-populations (ancestry groups such as Europeans or East Asians). You may want to do this as PopMax includes populations with low numbers (eg Finnish/Ashkenazi)
[PopMax](https://gnomad.broadinstitute.org/help/popmax) is the frequency of the highest sub-population (Note: gnomAD2 includes bottlenecked populations such as Finnish/Ashkenazi, while gnomADv3 excludes them)

Click "Pick individual gnomAD populations" to expand the selection to sub-populations (ancestry groups such as Europeans or East Asians).

You can also restrict to a max count (gnomAD hom alt or [internal zygosity counts]((../data/zygosity_counts.md))) which is useful to restrict to very rare variants (eg denovo)

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