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Update vcf-expression-annotator documentation to clarify custom id-column parameter #67

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Oct 16, 2023
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Update vcf-expression-annotator documentation to clarify custom id-column parameter #67

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Update vcf-expression-annotator documentation to clarify custom id-co…
susannasiebert Oct 12, 2023
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Fix grammar.
susannasiebert Oct 12, 2023
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7 changes: 4 additions & 3 deletions docs/vcf_expression_annotator.rst
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Expand Up @@ -22,16 +22,17 @@ file.

The VCF Expression Annotator also accepts a custom tab-delimited (TSV) file input for the
expression file. This TSV file will need to contain one column with gene or
transcripts identifiers and one column with the expression values. This file
transcripts Ensembl IDs and one column with the expression values. This file
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transcripts -> transcript

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then needs to contain a header line that is used to
identify the contents of each column. This is done via the ``--id-column``
and ``--expression-column`` parameters which need
to match the gene/transcript identifier and expression value column headers.
In order to use this option the expression file format option will need to be
set to ``custom``.
set to ``custom``. Please note that when running in ``gene`` mode, the ID
column will need to contain Ensembl Gene IDs, not gene names.

By default the output VCF will be written to a ``.tx.vcf`` or ``.gx.vcf`` file next to
your input VCF file. You can set a different output file using the
your input VCF file. You can set a different output file name using the
``--output-vcf`` parameter.

Usage
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