From c74b9f5733072e129b3457aadaea33e35449a555 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 12 Oct 2023 09:24:21 -0500 Subject: [PATCH 1/2] Update vcf-expression-annotator documentation to clarify custom id-column parameter --- docs/vcf_expression_annotator.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/vcf_expression_annotator.rst b/docs/vcf_expression_annotator.rst index 7dc3a9d..ec2fadd 100644 --- a/docs/vcf_expression_annotator.rst +++ b/docs/vcf_expression_annotator.rst @@ -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 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 From 9b02fb09821af82bc7a47f4b0e0303735aef64b5 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 12 Oct 2023 13:24:20 -0500 Subject: [PATCH 2/2] Fix grammar. --- docs/vcf_expression_annotator.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/vcf_expression_annotator.rst b/docs/vcf_expression_annotator.rst index ec2fadd..e5f7128 100644 --- a/docs/vcf_expression_annotator.rst +++ b/docs/vcf_expression_annotator.rst @@ -22,7 +22,7 @@ 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 Ensembl IDs and one column with the expression values. This file +transcrip Ensembl IDs and one column with the expression values. This file 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