From ed1a515075525cadff619c4c71a464299078faba Mon Sep 17 00:00:00 2001 From: ch-kr Date: Wed, 8 Nov 2023 14:27:35 -0500 Subject: [PATCH 1/5] Updated FAF to make it clearer that this field contains information about group with highest FAF, not FAF calculated on group with highest AF --- browser/help/topics/faf.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 8da9cb251..04de508a6 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -7,10 +7,10 @@ This annotation can be used for filtering variants by allele frequency against a This calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Genetic ancestry group specific AFs are listed separately with 95% and 99% CIs. +On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Genetic ancestry group specific filtering allele frequencies (FAFs) are listed separately with 95% and 99% CIs. -### Group maximum allele frequency +### Group maximum filtering allele frequency -This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest frequency. +This annotation (abbreviated "`grpmax FAF`") contains filtering allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest FAF. Note that this field contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. -For gnomAD v4, this excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (mid), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. +For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (mid), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. From 011305481fa3e1b5818d5b20ae97436c170cb5c6 Mon Sep 17 00:00:00 2001 From: Katherine Chao Date: Mon, 13 Nov 2023 09:48:32 -0500 Subject: [PATCH 2/5] Update browser/help/topics/faf.md Co-authored-by: klaricch --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 04de508a6..25824812c 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -13,4 +13,4 @@ On the browser, this annotation is directly available on the variant page. In th This annotation (abbreviated "`grpmax FAF`") contains filtering allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest FAF. Note that this field contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. -For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (mid), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. +For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. From edb4a57d1b056aed6afca0ed775e0cd7935ae31a Mon Sep 17 00:00:00 2001 From: Katherine Chao Date: Mon, 13 Nov 2023 09:48:44 -0500 Subject: [PATCH 3/5] Update browser/help/topics/faf.md Co-authored-by: klaricch --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 25824812c..dcc5015fc 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -7,7 +7,7 @@ This annotation can be used for filtering variants by allele frequency against a This calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Genetic ancestry group specific filtering allele frequencies (FAFs) are listed separately with 95% and 99% CIs. +On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs. ### Group maximum filtering allele frequency From 54d173bd372a2f3c57b830548fe2784decafe67e Mon Sep 17 00:00:00 2001 From: ch-kr Date: Mon, 13 Nov 2023 09:55:27 -0500 Subject: [PATCH 4/5] move note about faf, also update grpmax to be about grpmax --- browser/help/topics/faf.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index dcc5015fc..9af0f40c9 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -5,12 +5,14 @@ title: 'Filtering allele frequency' This annotation can be used for filtering variants by allele frequency against a disease-specific threshold that can be set for each disease (e.g. BA1 in the 2015 ACMG/AMP guidelines). In this case the filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (e.g. the lower bound of the 95% confidence interval (CI)). If the FAF is above the disease-specific threshold, then the observed AC is not compatible with pathogenicity. See http://cardiodb.org/allelefrequencyapp/ and [Whiffin _et al._ 2017](https://www.nature.com/articles/gim201726) for additional information. -This calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups. +Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. -On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs. +The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups. -### Group maximum filtering allele frequency +On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs. -This annotation (abbreviated "`grpmax FAF`") contains filtering allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest FAF. Note that this field contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. +### Group maximum allele frequency + +This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest **AF**. For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups. From b4993865be8c7e1474090016f3ff97d04ecf26c7 Mon Sep 17 00:00:00 2001 From: Katherine Chao Date: Mon, 13 Nov 2023 14:17:06 -0500 Subject: [PATCH 5/5] Update browser/help/topics/faf.md Co-authored-by: klaricch --- browser/help/topics/faf.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/browser/help/topics/faf.md b/browser/help/topics/faf.md index 9af0f40c9..25f300d58 100644 --- a/browser/help/topics/faf.md +++ b/browser/help/topics/faf.md @@ -7,7 +7,7 @@ This annotation can be used for filtering variants by allele frequency against a Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**. -The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups. +The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs.