From 1a9119bf934593609ec4a85eefeec653420a52f9 Mon Sep 17 00:00:00 2001 From: tgaspe Date: Wed, 28 Aug 2024 15:56:36 +0200 Subject: [PATCH] Update config.vsh.yaml --- src/bcftools/bcftools_annotate/config.vsh.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/bcftools/bcftools_annotate/config.vsh.yaml b/src/bcftools/bcftools_annotate/config.vsh.yaml index 6f5b23f0..3611dd18 100644 --- a/src/bcftools/bcftools_annotate/config.vsh.yaml +++ b/src/bcftools/bcftools_annotate/config.vsh.yaml @@ -97,7 +97,6 @@ argument_groups: Set ID column using a `bcftools query`-like expression, see man page for details. - name: --include - alternatives: --i type: string description: | Select sites for which the expression is true. @@ -133,22 +132,27 @@ argument_groups: - name: --no_version type: boolean_true description: | - Do not append version and command line information to the output VCF header.. + Do not append version and command line information to the output VCF header. - name: --output_type alternatives: --O type: string choices: ['u', 'z', 'b', 'v'] description: | - Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). + Output type: + u: uncompressed BCF + z: compressed VCF + b: compressed BCF + v: uncompressed VCF - name: --pair_logic type: string choices: ['snps', 'indels', 'both', 'all', 'some', 'exact'] description: | Controls how to match records from the annotation file to the target VCF. - Effective only when -a is a VCF or BCF. - The option replaces the former uninuitive --collapse. See Common Options for more. + Effective only when -a is a VCF or BCF file. + The option replaces the former uninuitive --collapse. + See Common Options for more. - name: --regions alternatives: --r