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Update to version 5.1.0
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susannasiebert committed Oct 16, 2023
1 parent 6dff9d7 commit 9084b09
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4 changes: 2 additions & 2 deletions docs/conf.py
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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 ---------------------------------------------------
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5 changes: 3 additions & 2 deletions docs/vcf_expression_annotator.rst
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Expand Up @@ -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
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6 changes: 4 additions & 2 deletions docs/vcf_readcount_annotator.rst
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Expand Up @@ -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
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5 changes: 4 additions & 1 deletion docs/vep_annotation_reporter.rst
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion setup.py
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setup(
name="vatools",
version="5.0.1",
version="5.1.0",
packages=["vatools"],
entry_points={
"console_scripts":[
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