From 9084b09dfa8bcde9cb1ebd47c1111b2240f2ecc5 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Mon, 16 Oct 2023 14:22:03 -0500 Subject: [PATCH] Update to version 5.1.0 --- docs/conf.py | 4 ++-- docs/vcf_expression_annotator.rst | 5 +++-- docs/vcf_readcount_annotator.rst | 6 ++++-- docs/vep_annotation_reporter.rst | 5 ++++- setup.py | 2 +- 5 files changed, 14 insertions(+), 8 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 2b31faa..7d78740 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -24,9 +24,9 @@ author = 'Susanna Kiwala, Chris Miller' # The short X.Y version -version = '5.0' +version = '5.1' # The full version, including alpha/beta/rc tags -release = '5.0.1' +release = '5.1.0' # -- General configuration --------------------------------------------------- diff --git a/docs/vcf_expression_annotator.rst b/docs/vcf_expression_annotator.rst index e5f7128..1d28846 100644 --- a/docs/vcf_expression_annotator.rst +++ b/docs/vcf_expression_annotator.rst @@ -11,8 +11,9 @@ be specified. This will result in the expression value to be written to the ``GX`` or ``TX`` field, respectively. The input VCF needs to be annotated with VEP with gene and transcript information so -that the VCF Expression Annotator can match a variant's gene and transcript -identifier in the VCF to the one in the expression file. Depending on the +that the VCF Expression Annotator can match a variant's Ensembl gene and transcript +identifier in the VCF to the one in the expression file. When running in +``gene`` mode, Ensembl IDs - not gene names - are used. Depending on the expression software used, the transcript identifiers might contain version numbers. To add transcript version numbers to your VEP annotation, use the ``--transcript_version`` when running VEP. You can also use the diff --git a/docs/vcf_readcount_annotator.rst b/docs/vcf_readcount_annotator.rst index 9ca651c..ba8edd9 100644 --- a/docs/vcf_readcount_annotator.rst +++ b/docs/vcf_readcount_annotator.rst @@ -7,11 +7,13 @@ and add its data to your VCF. It supports both DNA and RNA readcounts. DNA readcounts are identified by specifying ``DNA`` in the list of positional arguments. Depth, allele counts, and VAFs are then written to the -DP, AD, and AF fields, respectively. +DP, AD, and AF fields, respectively. Forward and reverse strand allele counts +are written in the ADF and ADR fields, respectively. RNA readcounts are identified by specifying ``RNA`` in the list of positional arguments. Depth, allele counts, and VAFs are then written tot he RDP, RAD, -and RAF fields, respectively. +and RAF fields, respectively. Forward and reverse strand allele counts +are written in the RADF and RADR fields, respectively. If your VCF is a multi-sample VCF, you have to pick one of the sample in your VCF by setting the ``--sample-name`` option. This is the sample that the diff --git a/docs/vep_annotation_reporter.rst b/docs/vep_annotation_reporter.rst index df18913..6d4e55e 100644 --- a/docs/vep_annotation_reporter.rst +++ b/docs/vep_annotation_reporter.rst @@ -19,7 +19,10 @@ values. This is the default behavior unless VEP was run with one of the ``--flag_pick`` options, all possible transcript consequences will be reported by VEP but only one of these consequences will be picked by VEP as the "best" consequence. This is denoted in the ``PICK`` field. If this field is -available, then the values for that transcript will be reported. +available, then the values for that transcript will be reported. For some +variants, VCFs annotated with the ``PICK`` field might not report any of the +consequences as picked. In that case, the values for all transcript consequences are +reported. VEP annotations can also be added to an existing TSV with variant information by using the ``--input-tsv`` option. In order to match diff --git a/setup.py b/setup.py index 37caa42..c51806f 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name="vatools", - version="5.0.1", + version="5.1.0", packages=["vatools"], entry_points={ "console_scripts":[