From 64c6a35f6bc156192bda96c957e4319ee84cec6f Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Mon, 20 Jan 2025 14:59:41 +0100 Subject: [PATCH] docu update --- doc/GSvar/changelog.md | 7 +++++++ doc/tools/TsvSlice.md | 6 ++++-- doc/tools/VariantFilterAnnotations.md | 6 +++--- doc/tools/VcfAdd.md | 20 ++++++++++---------- 4 files changed, 24 insertions(+), 15 deletions(-) diff --git a/doc/GSvar/changelog.md b/doc/GSvar/changelog.md index 7dd9d06fe..78662f1ef 100644 --- a/doc/GSvar/changelog.md +++ b/doc/GSvar/changelog.md @@ -1,5 +1,12 @@ # GSvar change log +## 2024_11-86 (20.01.25) + +- general: renamed class 'R*' to 'R' (changed in HerediCare and HerediVar) +- general: improved opening QC files from GSvarServer +- variant details: updated allOfUs variant URL +- NGSD: Added device type 'Revio' + ## 2024_11-50 (07.01.25) - general: added sample counts dialog (NGSD > Sample counts) diff --git a/doc/tools/TsvSlice.md b/doc/tools/TsvSlice.md index 761698615..a4278d9d9 100644 --- a/doc/tools/TsvSlice.md +++ b/doc/tools/TsvSlice.md @@ -1,5 +1,5 @@ ### TsvSlice tool help - TsvSlice (2024_08-113-g94a3b440) + TsvSlice (2024_11-86-g94c45dea) Extracts/reorders columns of a TSV file. @@ -13,6 +13,8 @@ Default value: '' -numeric If set, column names are interpreted as 1-based column numbers. Default value: 'false' + -rm If set, the columns given in 'cols' are removed instead of extracted. + Default value: 'false' Special parameters: --help Shows this help and exits. @@ -22,6 +24,6 @@ --settings [file] Settings override file (no other settings files are used). ### TsvSlice changelog - TsvSlice 2024_08-113-g94a3b440 + TsvSlice 2024_11-86-g94c45dea [back to ngs-bits](https://github.com/imgag/ngs-bits) \ No newline at end of file diff --git a/doc/tools/VariantFilterAnnotations.md b/doc/tools/VariantFilterAnnotations.md index 903ad2d29..a97050196 100644 --- a/doc/tools/VariantFilterAnnotations.md +++ b/doc/tools/VariantFilterAnnotations.md @@ -1,5 +1,5 @@ ### VariantFilterAnnotations tool help - VariantFilterAnnotations (2024_11-59-ge0a7288e) + VariantFilterAnnotations (2024_11-86-g94c45dea) Filter a variant list in GSvar format based on variant annotations. @@ -27,7 +27,7 @@ action - Action to perform [default=KEEP] [valid=KEEP,FILTER] Classification NGSD Filter for variant classification from NGSD. Parameters: - classes - NGSD classes [default=4,5] [valid=1,2,3,4,5,M,R*] [non-empty] + classes - NGSD classes [default=4,5] [valid=1,2,3,4,5,M,R] [non-empty] action - Action to perform [default=KEEP] [valid=KEEP,FILTER,REMOVE] Column match Filter that matches the content of a column against a perl-compatible regular expression. For details about regular expressions, see http://perldoc.perl.org/perlretut.html @@ -183,7 +183,7 @@ --settings [file] Settings override file (no other settings files are used). ### VariantFilterAnnotations changelog - VariantFilterAnnotations 2024_11-59-ge0a7288e + VariantFilterAnnotations 2024_11-86-g94c45dea 2018-07-30 Replaced command-line parameters by INI file and added many new filters. 2017-06-14 Refactoring of genotype-based filters: now also supports multi-sample filtering of affected and control samples. diff --git a/doc/tools/VcfAdd.md b/doc/tools/VcfAdd.md index f4553b49b..b35f61313 100644 --- a/doc/tools/VcfAdd.md +++ b/doc/tools/VcfAdd.md @@ -1,23 +1,22 @@ ### VcfAdd tool help - VcfAdd (2024_08-110-g317f43b9) + VcfAdd (2024_11-86-g94c45dea) - Appends variants from a VCF file to another VCF file. + Merges several VCF files into one VCF by appending one to the other. - VCF header lines are taken from 'in' only. + Variant lines from all other input files are appended to the first input file. + VCF header lines are taken from the first input file only. Mandatory parameters: - -in2 Input VCF file that is added to 'in'. + -in Input VCF ro VCG.GZ files to merge. Optional parameters: - -in Input VCF file to add 'in2' to. + -out Output VCF file with all variants. Default value: '' - -out Output VCF file with variants from 'in' and 'in2'. - Default value: '' - -filter Tag variants from 'in2' with this filter entry. + -filter Tag variants from all but the first input file with this filter entry. Default value: '' -filter_desc Description used in the filter header - use underscore instead of spaces. Default value: '' - -skip_duplicates Skip variants from 'in2' which are also contained in 'in'. + -skip_duplicates Skip variants if they occur more than once. Default value: 'false' Special parameters: @@ -28,7 +27,8 @@ --settings [file] Settings override file (no other settings files are used). ### VcfAdd changelog - VcfAdd 2024_08-110-g317f43b9 + VcfAdd 2024_11-86-g94c45dea + 2025-01-17 Added support for gzipped VCFs and removing duplicates if there is only one input file. 2022-12-08 Initial implementation. [back to ngs-bits](https://github.com/imgag/ngs-bits) \ No newline at end of file