From dcae41f6430e4b5d56aa11fb0036d0605c0b5598 Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Fri, 16 Dec 2022 13:25:51 +0100 Subject: [PATCH] Documentation update for release 2022_12 --- README.md | 22 +++++++++------------- doc/tools/NGSDUpdateSvGenotype.md | 24 ++++++++++++++++++++++++ doc/tools/SeqPurge.md | 6 +++--- doc/tools/VariantFilterAnnotations.md | 6 +++--- 4 files changed, 39 insertions(+), 19 deletions(-) create mode 100644 doc/tools/NGSDUpdateSvGenotype.md diff --git a/README.md b/README.md index 21b811e57..35542e575 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Alternatively, *ngs-bits* can be built from sources. Use git to clone the most r > git clone --recursive https://github.com/imgag/ngs-bits.git > cd ngs-bits - > git checkout 2022_10 + > git checkout 2022_12 > git submodule update --recursive --init Depending on your operating system, building instructions vary slightly: @@ -170,17 +170,13 @@ The default output format of the quality control tools is [qcML](https://pubmed. Changes of master since last release: -* GSvar: - * Updated ClinVar upload to new API version - * Added support to upload CNVs, SVs and CompHet variants to ClinVar - -Changes in release 2022_11: -* VcfAnnotateConsequence: implemented multi-threading, added much more tests and fixed several bugs. -* NGSDExportSamples: added filters for HPO terms and ancestry. -* NGSD: - * Added version number to table 'gene_transcript'. - * Updated tissue list in table 'sample'. - * Added comment field in table 'user'. - * Added DRAGEN as caller in table 'sv_callset'. +* none + +Changes in release 2022_12: + +* tool VcfAdd added +* VcfFilter: added option `-remove_invalid` +* VcfSort: added option `-remove_unused_contigs` +* VcfAnnotateConsequence: improved error handling and load time for GFF file For older changes see [releases](https://github.com/imgag/ngs-bits/releases). diff --git a/doc/tools/NGSDUpdateSvGenotype.md b/doc/tools/NGSDUpdateSvGenotype.md new file mode 100644 index 000000000..bc53e0ccc --- /dev/null +++ b/doc/tools/NGSDUpdateSvGenotype.md @@ -0,0 +1,24 @@ +### NGSDUpdateSvGenotype tool help + NGSDUpdateSvGenotype (2022_11-72-g9164a905) + + Updates the genotype for a given processed sample. + + Mandatory parameters: + -ps Processed sample id. + -in Input BEDPE file. + + Optional parameters: + -test Uses the test database instead of on the production database. + Default value: 'false' + + Special parameters: + --help Shows this help and exits. + --version Prints version and exits. + --changelog Prints changeloge and exits. + --tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'. + +### NGSDUpdateSvGenotype changelog + NGSDUpdateSvGenotype 2022_11-72-g9164a905 + + 2022-03-07 Initial commit. +[back to ngs-bits](https://github.com/imgag/ngs-bits) \ No newline at end of file diff --git a/doc/tools/SeqPurge.md b/doc/tools/SeqPurge.md index 42b8464c7..e04f42004 100644 --- a/doc/tools/SeqPurge.md +++ b/doc/tools/SeqPurge.md @@ -1,5 +1,5 @@ ### SeqPurge tool help - SeqPurge (2022_07-18-gfd880985) + SeqPurge (2022_11-72-g9164a905) Removes adapter sequences from paired-end sequencing data. @@ -17,7 +17,7 @@ -match_perc Minimum percentage of matching bases for sequence/adapter matches. Default value: '80' -mep Maximum error probability of insert and adapter matches. - Default value: '1e-6' + Default value: '1e-06' -qcut Quality trimming cutoff for trimming from the end of reads using a sliding window approach. Set to 0 to disable. Default value: '15' -qwin Quality trimming window size. @@ -56,7 +56,7 @@ --tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'. ### SeqPurge changelog - SeqPurge 2022_07-18-gfd880985 + SeqPurge 2022_11-72-g9164a905 2022-07-15 Improved scaling with more than 4 threads and CPU usage. 2019-03-26 Added 'compression_level' parameter. diff --git a/doc/tools/VariantFilterAnnotations.md b/doc/tools/VariantFilterAnnotations.md index 9a1c6ea3b..5e946e839 100644 --- a/doc/tools/VariantFilterAnnotations.md +++ b/doc/tools/VariantFilterAnnotations.md @@ -1,5 +1,5 @@ ### VariantFilterAnnotations tool help - VariantFilterAnnotations (2022_04-156-ga57fe9df) + VariantFilterAnnotations (2022_11-72-g9164a905) Filter a variant list in GSvar format based on variant annotations. @@ -59,7 +59,7 @@ min_pli - Minumum ExAC pLI score [default=0.9] [min=0.0] [max=1.0] Gene inheritance Filter based on gene inheritance. Parameters: - modes - Inheritance mode(s) [valid=AR,AD,XLR,XLD,MT] [non-empty] + modes - Inheritance mode(s) [valid=AR,AD,XLR,XLD,MT,n/a] [non-empty] Genes Filter that preserves a gene set. Parameters: genes - Gene set [non-empty] @@ -173,7 +173,7 @@ --tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'. ### VariantFilterAnnotations changelog - VariantFilterAnnotations 2022_04-156-ga57fe9df + VariantFilterAnnotations 2022_11-72-g9164a905 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.