From bcd4498413c5779435b128c4a020d9f3a48ee2a9 Mon Sep 17 00:00:00 2001 From: Likhitha Surapaneni <10923198+likhitha-surapaneni@users.noreply.github.com> Date: Tue, 6 Aug 2024 13:27:11 +0100 Subject: [PATCH 1/6] Updating docs for gencode_primary --- .../info/docs/tools/vep/online/input.html | 5 +++++ .../docs/tools/vep/script/vep_options.html | 20 +++++++++++++++++++ .../info/docs/tools/vep/vep_formats.html | 1 + 3 files changed, 26 insertions(+) diff --git a/docs/htdocs/info/docs/tools/vep/online/input.html b/docs/htdocs/info/docs/tools/vep/online/input.html index 3313f5a30..ea5bb4860 100644 --- a/docs/htdocs/info/docs/tools/vep/online/input.html +++ b/docs/htdocs/info/docs/tools/vep/online/input.html @@ -79,6 +79,11 @@

Data input

majority of users. GENCODE Basic includes all genes in the GENCODE gene set, with a representative subset of the transcripts (splice variants).

+

GENCODE Primary is a new transcript subset which covers + all human exons in a minimal set of transcripts. + This aims to enable annotation of all potential variant + consequences without duplication across multiple transcripts +

You can also select to use RefSeq transcripts from the otherfeatures database; note though that these transcripts are simply diff --git a/docs/htdocs/info/docs/tools/vep/script/vep_options.html b/docs/htdocs/info/docs/tools/vep/script/vep_options.html index 055ad3f74..a18582a42 100644 --- a/docs/htdocs/info/docs/tools/vep/script/vep_options.html +++ b/docs/htdocs/info/docs/tools/vep/script/vep_options.html @@ -1701,6 +1701,18 @@

Filtering and QC options

--refseq
+ + 
--gencode_primary
+   + + Limit your analysis to transcripts belonging to the GENCODE + Primary set. This set covers all human exons in a minimal set of transcripts Not used by default + +   + +
--refseq
+ + 
--exclude_predicted
  @@ -1995,6 +2007,14 @@

Note

--vcf
+ + 
--flag_gencode_primary
+   + + Flags transcripts as GENCODE primary using a boolean value Not used by default + + GENCODE_PRIMARY + 
--filter_common
  diff --git a/docs/htdocs/info/docs/tools/vep/vep_formats.html b/docs/htdocs/info/docs/tools/vep/vep_formats.html index 18a097e7a..c0262651c 100644 --- a/docs/htdocs/info/docs/tools/vep/vep_formats.html +++ b/docs/htdocs/info/docs/tools/vep/vep_formats.html @@ -612,6 +612,7 @@

Other output fields:

  • BIOTYPE - Biotype of transcript or regulatory feature
  • APPRIS - Annotates alternatively spliced transcripts as primary or alternate based on a range of computational methods. NB: not available for GRCh37
  • TSL - Transcript support level. NB: not available for GRCh37
    • +
  • GENCODE_PRIMARY - Reports if transcript belongs to GENCODE Primary subset
  • PUBMED - Pubmed ID(s) of publications that cite existing variant
  • SOMATIC - Somatic status of existing variant(s); multiple values correspond to multiple values in the Existing_variation field
  • PHENO - Indicates if existing variant is associated with a phenotype, disease or trait; multiple values correspond to multiple values in the Existing_variation field
    • From 4d75a2666872103e50d002bd35c2e8ffc29dc8af Mon Sep 17 00:00:00 2001 From: Likhitha Surapaneni <10923198+likhitha-surapaneni@users.noreply.github.com> Date: Tue, 6 Aug 2024 13:44:28 +0100 Subject: [PATCH 2/6] Modified form-related docs --- docs/htdocs/info/docs/tools/vep/online/input.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/htdocs/info/docs/tools/vep/online/input.html b/docs/htdocs/info/docs/tools/vep/online/input.html index ea5bb4860..c39072fd3 100644 --- a/docs/htdocs/info/docs/tools/vep/online/input.html +++ b/docs/htdocs/info/docs/tools/vep/online/input.html @@ -120,7 +120,7 @@

    Data input

    Or provide file URL:
    -

    +

    @@ -516,7 +516,7 @@

    Transcript annotation

    -

    +

    @@ -526,14 +526,14 @@

    Transcript annotation

    Protein annotation

    -

    +

    Functional effect

    -

    +

    From 27f4c0f4e1019e9671a162623a8f640ebff9daaf Mon Sep 17 00:00:00 2001 From: Likhitha Surapaneni <10923198+likhitha-surapaneni@users.noreply.github.com> Date: Tue, 6 Aug 2024 13:48:20 +0100 Subject: [PATCH 3/6] Minor changes --- docs/htdocs/info/docs/tools/vep/script/vep_options.html | 2 +- docs/htdocs/info/docs/tools/vep/vep_formats.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/htdocs/info/docs/tools/vep/script/vep_options.html b/docs/htdocs/info/docs/tools/vep/script/vep_options.html index a18582a42..ab092df89 100644 --- a/docs/htdocs/info/docs/tools/vep/script/vep_options.html +++ b/docs/htdocs/info/docs/tools/vep/script/vep_options.html @@ -1706,7 +1706,7 @@

    Filtering and QC options

      Limit your analysis to transcripts belonging to the GENCODE - Primary set. This set covers all human exons in a minimal set of transcripts Not used by default + primary set. This set covers all human exons in a minimal set of transcripts Not used by default   diff --git a/docs/htdocs/info/docs/tools/vep/vep_formats.html b/docs/htdocs/info/docs/tools/vep/vep_formats.html index c0262651c..cd7681dbd 100644 --- a/docs/htdocs/info/docs/tools/vep/vep_formats.html +++ b/docs/htdocs/info/docs/tools/vep/vep_formats.html @@ -612,7 +612,7 @@

    Other output fields:

  • BIOTYPE - Biotype of transcript or regulatory feature
  • APPRIS - Annotates alternatively spliced transcripts as primary or alternate based on a range of computational methods. NB: not available for GRCh37
  • TSL - Transcript support level. NB: not available for GRCh37
    • -
  • GENCODE_PRIMARY - Reports if transcript belongs to GENCODE Primary subset
    • +
  • GENCODE_PRIMARY - Reports if transcript belongs to GENCODE primary subset
  • PUBMED - Pubmed ID(s) of publications that cite existing variant
  • SOMATIC - Somatic status of existing variant(s); multiple values correspond to multiple values in the Existing_variation field
  • PHENO - Indicates if existing variant is associated with a phenotype, disease or trait; multiple values correspond to multiple values in the Existing_variation field
    • From cd0f1830b0f84c3c681b8a27c491ba46cf38aef5 Mon Sep 17 00:00:00 2001 From: Likhitha Surapaneni <10923198+likhitha-surapaneni@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:14:13 +0100 Subject: [PATCH 4/6] Minor style changes --- docs/htdocs/info/docs/tools/vep/online/input.html | 4 ++-- docs/htdocs/info/docs/tools/vep/script/vep_options.html | 8 ++++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/docs/htdocs/info/docs/tools/vep/online/input.html b/docs/htdocs/info/docs/tools/vep/online/input.html index c39072fd3..bd48725c2 100644 --- a/docs/htdocs/info/docs/tools/vep/online/input.html +++ b/docs/htdocs/info/docs/tools/vep/online/input.html @@ -82,7 +82,7 @@

    Data input

    GENCODE Primary is a new transcript subset which covers all human exons in a minimal set of transcripts. This aims to enable annotation of all potential variant - consequences without duplication across multiple transcripts + consequences without duplication across multiple transcripts.

    You can also select to use RefSeq transcripts from the otherfeatures @@ -120,7 +120,7 @@

    Data input

    Or provide file URL:
    -

    +

    diff --git a/docs/htdocs/info/docs/tools/vep/script/vep_options.html b/docs/htdocs/info/docs/tools/vep/script/vep_options.html index ab092df89..a0fb8ab6f 100644 --- a/docs/htdocs/info/docs/tools/vep/script/vep_options.html +++ b/docs/htdocs/info/docs/tools/vep/script/vep_options.html @@ -490,6 +490,7 @@

    Cache options

    REFSEQ_MATCH, BAM_EDIT
    --gencode_basic
    +
    --gencode_primary
    --merged
    @@ -1698,6 +1699,7 @@

    Filtering and QC options

      +
    --gencode_primary
    --refseq
    @@ -1706,10 +1708,11 @@

    Filtering and QC options

      Limit your analysis to transcripts belonging to the GENCODE - primary set. This set covers all human exons in a minimal set of transcripts Not used by default + primary set. This set covers all human exons in a minimal set of transcripts. Not used by default   +
    --gencode_basic
    --refseq
    @@ -2011,9 +2014,10 @@

    Note

    --flag_gencode_primary
      - Flags transcripts as GENCODE primary using a boolean value Not used by default + Flags transcripts as GENCODE primary using a boolean value. Not used by default GENCODE_PRIMARY +   
    --filter_common
    From ec512bbe80a378ee89316d1747e08f61a2628f86 Mon Sep 17 00:00:00 2001 From: Likhitha Surapaneni <10923198+likhitha-surapaneni@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:25:23 +0100 Subject: [PATCH 5/6] Minor style changes --- docs/htdocs/info/docs/tools/vep/online/input.html | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/htdocs/info/docs/tools/vep/online/input.html b/docs/htdocs/info/docs/tools/vep/online/input.html index bd48725c2..d60133576 100644 --- a/docs/htdocs/info/docs/tools/vep/online/input.html +++ b/docs/htdocs/info/docs/tools/vep/online/input.html @@ -119,8 +119,7 @@

    Data input

    Or provide file URL:
    - -

    +

    From 3ecc21202abeaf737d76979baf49c166765e6254 Mon Sep 17 00:00:00 2001 From: Likhitha Surapaneni <10923198+likhitha-surapaneni@users.noreply.github.com> Date: Tue, 6 Aug 2024 15:57:12 +0100 Subject: [PATCH 6/6] Added note that options work on human grch38 only --- .../info/docs/tools/vep/script/vep_options.html | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/docs/htdocs/info/docs/tools/vep/script/vep_options.html b/docs/htdocs/info/docs/tools/vep/script/vep_options.html index a0fb8ab6f..de5cc1369 100644 --- a/docs/htdocs/info/docs/tools/vep/script/vep_options.html +++ b/docs/htdocs/info/docs/tools/vep/script/vep_options.html @@ -1709,6 +1709,12 @@

    Filtering and QC options

    Limit your analysis to transcripts belonging to the GENCODE primary set. This set covers all human exons in a minimal set of transcripts. Not used by default +
    +

    Note

    +
    + Only available for human on the GRCh38 assembly +
    +
      @@ -2015,6 +2021,12 @@

    Note

      Flags transcripts as GENCODE primary using a boolean value. Not used by default +
    +

    Note

    +
    + Only available for human on the GRCh38 assembly +
    +
    GENCODE_PRIMARY