From c5150c565522c96a0f8ce97e5a21680f54054552 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 12:37:26 +0200 Subject: [PATCH 01/15] fix command in vcf2cytosure rule and update ReadtheDocs --- .../annotation/vcf2cytosure_convert.rule | 2 +- docs/FAQs.rst | 56 ----------------- docs/balsamic_sv_cnv.rst | 61 ++++++++++++++++++- docs/cli_package.rst | 2 +- docs/conf.py | 2 +- docs/history.rst | 2 +- docs/index.rst | 6 +- docs/resources.rst | 5 +- 8 files changed, 68 insertions(+), 68 deletions(-) diff --git a/BALSAMIC/snakemake_rules/annotation/vcf2cytosure_convert.rule b/BALSAMIC/snakemake_rules/annotation/vcf2cytosure_convert.rule index 51d5ba88b..cc3110cdd 100644 --- a/BALSAMIC/snakemake_rules/annotation/vcf2cytosure_convert.rule +++ b/BALSAMIC/snakemake_rules/annotation/vcf2cytosure_convert.rule @@ -70,7 +70,7 @@ elif config["analysis"]["sequencing_type"] == "wgs" and config["analysis"]["anal message: "Converting CNVs from VCF to the CGH format using vcf2cytosure for {params.case_name}" shell: """ -grep -E "#|PASS" {input.ascat_vcf} | bgzip -l 9 -c > {output.ascat_vcf}; +zgrep -E "#|PASS" {input.ascat_vcf} | bgzip -l 9 -c > {output.ascat_vcf}; vcf2cytosure --vcf {output.ascat_vcf} --coverage {input.tiddit_cov_tumor} --out {output.cgh_tumor} --sex {params.gender} --bins 20 diff --git a/docs/FAQs.rst b/docs/FAQs.rst index e712acf41..f0ea33aa5 100644 --- a/docs/FAQs.rst +++ b/docs/FAQs.rst @@ -96,59 +96,3 @@ Make a pull request to master at this point. After pull request is approved and - Never force rebase commits into either `master` or `develop` branches. - When merging pull requests commits into `master` branch, use **Create a merge commit**, which helps to capture all the commit history. On contrary, when merging pull requests into `develop` branch, use **Squash and merge** button, which combines multiple commits messages into one commit. -**References** -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -**How to generate reference files for ascatNGS** - -Detailed information is available from `ascatNGS `_ documentation - -Briefly, ascatNGS needs gender loci file if gender information for the input sample is not available. The second file is *SnpGcCorrections.tsv*, which is prepared from the 1000 genome SNP panel. - -1. **Gender loci file:** - -GRCh37d5_Y.loci contains the following contents: - -.. line-block:: - Y 4546684 - Y 2934912 - Y 4550107 - Y 4549638 - - -2. **GC correction file:** - -First step is to download the 1000 genome snp file and convert it from .vcf to .tsv. The detailed procedure to for this step is available from `ascatNGS-reference-files `_ (Human reference files from 1000 genomes VCFs) - -.. code-block:: - - export TG_DATA=ftp://ftp.ensembl.org/pub/grch37/release-83/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz - - -Followed by: - -.. code-block:: - - curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\ - perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/);\ - next if($F[0] eq $l_c && $F[1]-1000 < $l_p); $F[7]=~m/MAF=([^;]+)/;\ - next if($1 < 0.05); printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1];\ - $l_c=$F[0]; $l_p=$F[1];' > SnpPositions_GRCh37_1000g.tsv - - ---or-- - -.. code-block:: - - curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\ - perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/); $F[7]=~m/MAF=([^;]+)/;\ - next if($1 < 0.05); next if($F[0] eq $l_c && $F[1]-1000 < $l_p);\ - printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1]; $l_c=$F[0]; $l_p=$F[1];'\ - > SnpPositions_GRCh37_1000g.tsv - -Second step is to use *SnpPositions.tsv* file and generate *SnpGcCorrections.tsv* file, more details see `ascatNGS-convert-snppositions `_ - -.. code-block:: - - ascatSnpPanelGcCorrections.pl genome.fa SnpPositions.tsv > SnpGcCorrections.tsv - diff --git a/docs/balsamic_sv_cnv.rst b/docs/balsamic_sv_cnv.rst index 82529b7c4..bdcb7d752 100644 --- a/docs/balsamic_sv_cnv.rst +++ b/docs/balsamic_sv_cnv.rst @@ -81,4 +81,63 @@ The following command can be used to fetch the variants identified by a specific :: - zgrep -E "#|" <*.svdb.vcf.gz> \ No newline at end of file + zgrep -E "#|" <*.svdb.vcf.gz> + + + +**Genome Reference Files** +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +**How to generate genome reference files for ascatNGS** + +Detailed information is available from `ascatNGS `_ documentation + +Briefly, ascatNGS needs gender loci file if gender information for the input sample is not available. The second file is *SnpGcCorrections.tsv*, which is prepared from the 1000 genome SNP panel. + +1. **Gender loci file:** + +GRCh37d5_Y.loci contains the following contents: + +.. line-block:: + Y 4546684 + Y 2934912 + Y 4550107 + Y 4549638 + + +2. **GC correction file:** + +First step is to download the 1000 genome snp file and convert it from .vcf to .tsv. The detailed procedure to for this step is available from `ascatNGS-reference-files `_ (Human reference files from 1000 genomes VCFs) + +.. code-block:: + + export TG_DATA=ftp://ftp.ensembl.org/pub/grch37/release-83/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz + + +Followed by: + +.. code-block:: + + curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\ + perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/);\ + next if($F[0] eq $l_c && $F[1]-1000 < $l_p); $F[7]=~m/MAF=([^;]+)/;\ + next if($1 < 0.05); printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1];\ + $l_c=$F[0]; $l_p=$F[1];' > SnpPositions_GRCh37_1000g.tsv + + +--or-- + +.. code-block:: + + curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\ + perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/); $F[7]=~m/MAF=([^;]+)/;\ + next if($1 < 0.05); next if($F[0] eq $l_c && $F[1]-1000 < $l_p);\ + printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1]; $l_c=$F[0]; $l_p=$F[1];'\ + > SnpPositions_GRCh37_1000g.tsv + +Second step is to use *SnpPositions.tsv* file and generate *SnpGcCorrections.tsv* file, more details see `ascatNGS-convert-snppositions `_ + +.. code-block:: + + ascatSnpPanelGcCorrections.pl genome.fa SnpPositions.tsv > SnpGcCorrections.tsv + diff --git a/docs/cli_package.rst b/docs/cli_package.rst index e446f96a7..c2245cb07 100644 --- a/docs/cli_package.rst +++ b/docs/cli_package.rst @@ -4,4 +4,4 @@ CLI reference .. click:: BALSAMIC.commands.base:cli :prog: BALSAMIC - :show-nested: + :nested: full diff --git a/docs/conf.py b/docs/conf.py index 34a287b69..475b45443 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -31,7 +31,7 @@ "sphinx.ext.mathjax", "sphinx.ext.viewcode", "sphinxcontrib.napoleon", - "sphinx_click.ext", + "sphinx_click", "sphinxarg.ext", "recommonmark", ] diff --git a/docs/history.rst b/docs/history.rst index 12ee6b6f1..4de03af31 100644 --- a/docs/history.rst +++ b/docs/history.rst @@ -1,4 +1,4 @@ -CHANGELOG +Changelog ========= .. include:: ../CHANGELOG.rst diff --git a/docs/index.rst b/docs/index.rst index b4aca47b4..51cb6e093 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -11,8 +11,8 @@ .. toctree:: - :caption: Resources - :name: resources + :caption: Tools and Resources + :name: tools and resources :hidden: :maxdepth: 1 @@ -21,6 +21,7 @@ balsamic_annotation balsamic_methods bioinfo_softwares + resources .. toctree:: @@ -38,7 +39,6 @@ :maxdepth: 1 history - resources .. toctree:: :caption: Development guide diff --git a/docs/resources.rst b/docs/resources.rst index b8839a9f9..cef6503f2 100644 --- a/docs/resources.rst +++ b/docs/resources.rst @@ -1,11 +1,8 @@ =============== -Other resources +References =============== -Resources ---------- - *Main resources including knowledge base and databases necessary for pipeline development* From fe30ba1b17d4d4583a2a14228f1715a43cc27033 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 12:37:52 +0200 Subject: [PATCH 02/15] fix command in vcf2cytosure rule and update ReadtheDocs --- CHANGELOG.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f0b8c8a3b..2da0a6312 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -37,6 +37,7 @@ Fixed: * `run_validate.sh` script https://github.com/Clinical-Genomics/BALSAMIC/pull/952 * Somatic SV tumor normal rules https://github.com/Clinical-Genomics/BALSAMIC/pull/959 * Missing `genderChr` flag for `ascat_tumor_normal` rule https://github.com/Clinical-Genomics/BALSAMIC/pull/963 +* Command in vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/965 Removed ^^^^^^^ From 17fdb92087d0380aa3f52cfe07d44f609f8e620a Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 13:48:56 +0200 Subject: [PATCH 03/15] fix spinx.click --- CHANGELOG.rst | 2 +- docs/balsamic_sv_cnv.rst | 17 ++++------------- docs/conf.py | 2 +- docs/requirements.txt | 2 +- 4 files changed, 7 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 2da0a6312..76690aa1a 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -37,7 +37,7 @@ Fixed: * `run_validate.sh` script https://github.com/Clinical-Genomics/BALSAMIC/pull/952 * Somatic SV tumor normal rules https://github.com/Clinical-Genomics/BALSAMIC/pull/959 * Missing `genderChr` flag for `ascat_tumor_normal` rule https://github.com/Clinical-Genomics/BALSAMIC/pull/963 -* Command in vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/965 +* Command in vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966 Removed ^^^^^^^ diff --git a/docs/balsamic_sv_cnv.rst b/docs/balsamic_sv_cnv.rst index bdcb7d752..77c421ea3 100644 --- a/docs/balsamic_sv_cnv.rst +++ b/docs/balsamic_sv_cnv.rst @@ -42,6 +42,8 @@ Depending on the sequencing type, BALSAMIC is currently running the following st Further details about a specific caller can be found in the links for the repositories containing the documentation for SV and CNV callers along with the links for the articles are listed in `bioinfo softwares `_. +It mandatory to provide the gender of the sample from BALSAMIC version >= 10.0.0 For CNV analysis. + The copy number variants, identified using ascatNgs and `dellycnv`, are converted to deletion and duplications before they are merged using `SVDB` with `--bnd_distance = 5000` (distance between end points for the variants from different callers) and `--overlap = 0.80` (percentage for overlapping bases for the variants from different callers). `SVDB` prioritizes the merging of variants from SV and CNV callers to fetch position and genotype information, in the following order: .. list-table:: SVDB merge caller priority order @@ -92,20 +94,9 @@ The following command can be used to fetch the variants identified by a specific Detailed information is available from `ascatNGS `_ documentation -Briefly, ascatNGS needs gender loci file if gender information for the input sample is not available. The second file is *SnpGcCorrections.tsv*, which is prepared from the 1000 genome SNP panel. - -1. **Gender loci file:** - -GRCh37d5_Y.loci contains the following contents: - -.. line-block:: - Y 4546684 - Y 2934912 - Y 4550107 - Y 4549638 - +The file *SnpGcCorrections.tsv* prepared from the 1000 genome SNP panel. -2. **GC correction file:** +**GC correction file:** First step is to download the 1000 genome snp file and convert it from .vcf to .tsv. The detailed procedure to for this step is available from `ascatNGS-reference-files `_ (Human reference files from 1000 genomes VCFs) diff --git a/docs/conf.py b/docs/conf.py index 475b45443..8b5020b6e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,7 +13,7 @@ import os import sys -sys.path.insert(0, os.path.abspath("../")) +sys.path.insert(0, os.path.abspath("..")) # -- Project information ----------------------------------------------------- diff --git a/docs/requirements.txt b/docs/requirements.txt index 2fefe4578..77590bced 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -4,7 +4,7 @@ docutils>=0.14,<0.18 recommonmark==0.7.1 sphinx==4.2.0 sphinx-argparse==0.3.1 -sphinx-click==3.0.1 +sphinx-click==3.0.2 sphinx_rtd_theme==1.0.0 sphinxcontrib-napoleon==0.7 furo==2021.10.9 From c8ccb081c26d5e0b48bedead2db001668f364ac6 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 18:06:01 +0200 Subject: [PATCH 04/15] restructure and reheader ReadtheDocs --- docs/README.rst | 2 +- docs/balsamic_annotation.rst | 2 +- docs/balsamic_methods.rst | 6 +++--- docs/bioinfo_softwares.rst | 2 +- docs/cli_package.rst | 2 +- docs/git_etiquette.rst | 2 +- docs/index.rst | 21 ++++----------------- docs/snakemake_etiquette.rst | 2 +- 8 files changed, 13 insertions(+), 26 deletions(-) diff --git a/docs/README.rst b/docs/README.rst index 2872ebd20..5a7737b74 100644 --- a/docs/README.rst +++ b/docs/README.rst @@ -1,5 +1,5 @@ ========= -Build Doc +Build doc ========= Following steps explains how to build documents locally. diff --git a/docs/balsamic_annotation.rst b/docs/balsamic_annotation.rst index 8c19e2326..0a5b932ed 100644 --- a/docs/balsamic_annotation.rst +++ b/docs/balsamic_annotation.rst @@ -1,5 +1,5 @@ *********************************** -Annotation Resources +Annotation resources *********************************** BALSAMIC annotates somatic single nucleotide variants (SNVs) using ``ensembl-vep`` and ``vcfanno``. Somatic structural variants (SVs), somatic copy-number variants (CNVs) and germline single nucleotide variants are annotated using only ``ensembl-vep``. All SVs and CNVs are merged using ``SVDB`` before annotating for `Target Genome Analysis (TGA)` or `Whole Genome Sequencing (WGS)` analyses. diff --git a/docs/balsamic_methods.rst b/docs/balsamic_methods.rst index a51b18a3d..ee1bab85c 100644 --- a/docs/balsamic_methods.rst +++ b/docs/balsamic_methods.rst @@ -1,6 +1,6 @@ -======== -Methods -======== +=================== +Method description +=================== Target Genome Analysis ~~~~~~~~~~~~~~~~~~~~~~ diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst index b172ec17d..8a806e55c 100644 --- a/docs/bioinfo_softwares.rst +++ b/docs/bioinfo_softwares.rst @@ -1,5 +1,5 @@ ================================= -List of bioinformatics software +Tools and software ================================= BALSAMIC ( **version** = 9.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each diff --git a/docs/cli_package.rst b/docs/cli_package.rst index c2245cb07..2a6b58972 100644 --- a/docs/cli_package.rst +++ b/docs/cli_package.rst @@ -1,5 +1,5 @@ ============= -CLI reference +CLI usage ============= .. click:: BALSAMIC.commands.base:cli diff --git a/docs/git_etiquette.rst b/docs/git_etiquette.rst index 4c285806f..d72ed3b62 100644 --- a/docs/git_etiquette.rst +++ b/docs/git_etiquette.rst @@ -1,5 +1,5 @@ ============= -Git Etiquette +Git etiquette ============= It is recommended to follow a system to standardize the commit messages loosely. Following up from commit messages discussed on https://github.com/Clinical-Genomics/development/pull/97 , the format below is recommended for commit messages: diff --git a/docs/index.rst b/docs/index.rst index 51cb6e093..f781f6e46 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -8,11 +8,12 @@ install user_guide + cli_package .. toctree:: - :caption: Tools and Resources - :name: tools and resources + :caption: Detailed documentation + :name: detailed documentation :hidden: :maxdepth: 1 @@ -21,24 +22,10 @@ balsamic_annotation balsamic_methods bioinfo_softwares + history resources -.. toctree:: - :caption: CLI reference - :name: api_cli_reference - :hidden: - :maxdepth: 1 - - cli_package - -.. toctree:: - :caption: Other Info - :name: other_info - :hidden: - :maxdepth: 1 - - history .. toctree:: :caption: Development guide diff --git a/docs/snakemake_etiquette.rst b/docs/snakemake_etiquette.rst index 462a93ce9..27b064770 100644 --- a/docs/snakemake_etiquette.rst +++ b/docs/snakemake_etiquette.rst @@ -1,5 +1,5 @@ =================== -Snakemake Etiquette +Snakemake etiquette =================== The bioinformatics core analysis in BALSAMIC is defined by set of rules written as a Snakemake rules (``*.rule``) and Snakemake From 831626605b46eb4d9648f197e1558dfa6395886e Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 18:15:19 +0200 Subject: [PATCH 05/15] restructure and reheader ReadtheDocs --- docs/balsamic_filters.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst index 83b8125b7..47033edf5 100644 --- a/docs/balsamic_filters.rst +++ b/docs/balsamic_filters.rst @@ -1,5 +1,5 @@ *********************************** -Calling and Filtering Variants +Calling and filtering Variants *********************************** In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants. Also, the choice of these tools differs between the type of analysis, From bf199f9cae65ee01d30a2af7027e535f30a53db5 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 22:43:05 +0200 Subject: [PATCH 06/15] format header --- docs/balsamic_filters.rst | 50 ++++++++++++++++++++++++++++++++++++--- docs/balsamic_sv_cnv.rst | 2 +- 2 files changed, 48 insertions(+), 4 deletions(-) diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst index 47033edf5..143276d6c 100644 --- a/docs/balsamic_filters.rst +++ b/docs/balsamic_filters.rst @@ -1,9 +1,53 @@ *********************************** -Calling and filtering Variants +Calling and filtering variants *********************************** -In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants. Also, the choice of these tools differs between the type of analysis, -e.g.: `Target Genome Analysis (TGA)` or analysis of `Whole Genome Sequencing (WGS)`. Various filters (Pre-call and Post-call filtering) are applied at different levels to report high-confidence variant calls. +In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants summarized in the table below. The choice of these tools differs between the type of analysis, +e.g.: `Target Genome Analysis (TGA)` or analysis of `Whole Genome Sequencing (WGS)`. + + +.. list-table:: SNV and small-Indel callers + :widths: 23 27 25 25 25 + :header-rows: 1 + + * - Variant caller + - Sequencing type + - Analysis type + - Somatic/Germline + - Variant type + * - DNAScope + - WGS + - tumor-normal, tumor-only + - germline + - SNVs, InDels + * - TNhaplotyper + - TGA, WES, WGS :superscript:`1` + - tumor-normal, tumor-only + - somatic + - SNVs, InDels + * - TNScope :superscript:`2` + - WGS + - tumor-normal, tumor-only + - somatic + - SNVs, InDels + * - TNScope_umi + - TGA, WGS + - tumor-normal, tumor-only + - somatic, germline + - SNVs, InDels + * - VarDict + - TGA, WGS + - tumor-normal, tumor-only + - somatic + - SNVs, InDels + +:superscript:`1` TNhaplotyper is only executed for tumor-only if a WGS case is being analysed + +:superscript:`2` TNScope output is being merged with TNhaplotyper calls for TO-WGS analysis + + + +Various filters (Pre-call and Post-call filtering) are applied at different levels to report high-confidence variant calls. **Pre-call filtering** is where the variant-calling tool decides not to add a variant to the VCF file if the default filters of the variant-caller did not pass the filter criteria. The set of default filters differs between the various variant-calling algorithms. diff --git a/docs/balsamic_sv_cnv.rst b/docs/balsamic_sv_cnv.rst index 77c421ea3..2275f8d92 100644 --- a/docs/balsamic_sv_cnv.rst +++ b/docs/balsamic_sv_cnv.rst @@ -1,5 +1,5 @@ ************************************ -Structural and Copy Number Variants +Structural and copy-number variants ************************************ Depending on the sequencing type, BALSAMIC is currently running the following structural and copy number variant callers: From ccf3b42cce66477eee309c0dd9b1356945ef4eee Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 22:43:22 +0200 Subject: [PATCH 07/15] add SVN small indel table --- docs/balsamic_filters.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst index 143276d6c..47b3ac9f7 100644 --- a/docs/balsamic_filters.rst +++ b/docs/balsamic_filters.rst @@ -2,8 +2,7 @@ Calling and filtering variants *********************************** -In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants summarized in the table below. The choice of these tools differs between the type of analysis, -e.g.: `Target Genome Analysis (TGA)` or analysis of `Whole Genome Sequencing (WGS)`. +In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants summarized in the table below. The choice of these tools differs between the type of analysis, `Target Genome Analysis (TGA)` or analysis of `Whole Genome Sequencing (WGS)`. .. list-table:: SNV and small-Indel callers From 6e7edcda20d0579a63a0ffe46694aecba344434f Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 22:49:08 +0200 Subject: [PATCH 08/15] format table --- docs/balsamic_filters.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst index 47b3ac9f7..089126ef5 100644 --- a/docs/balsamic_filters.rst +++ b/docs/balsamic_filters.rst @@ -6,7 +6,7 @@ In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germ .. list-table:: SNV and small-Indel callers - :widths: 23 27 25 25 25 + :widths: 22 27 25 20 20 :header-rows: 1 * - Variant caller @@ -18,27 +18,27 @@ In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germ - WGS - tumor-normal, tumor-only - germline - - SNVs, InDels + - SNV, InDel * - TNhaplotyper - TGA, WES, WGS :superscript:`1` - tumor-normal, tumor-only - somatic - - SNVs, InDels + - SNV, InDel * - TNScope :superscript:`2` - WGS - tumor-normal, tumor-only - somatic - - SNVs, InDels + - SNV, InDel * - TNScope_umi - TGA, WGS - tumor-normal, tumor-only - somatic, germline - - SNVs, InDels + - SNV, InDel * - VarDict - TGA, WGS - tumor-normal, tumor-only - somatic - - SNVs, InDels + - SNV, InDel :superscript:`1` TNhaplotyper is only executed for tumor-only if a WGS case is being analysed From 51e0e05c68760d1c3eda05f82f89fcbc50a00c9e Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 22:55:11 +0200 Subject: [PATCH 09/15] move other resources --- docs/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index f781f6e46..7124a2512 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -21,9 +21,8 @@ balsamic_sv_cnv balsamic_annotation balsamic_methods - bioinfo_softwares history - resources + bioinfo_softwares @@ -38,3 +37,4 @@ README semver FAQs + resources From d43bf102f8b1abd975bf031bd004e0ac0f17d80a Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 22:55:27 +0200 Subject: [PATCH 10/15] reheader --- docs/resources.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/resources.rst b/docs/resources.rst index cef6503f2..7ebe1c640 100644 --- a/docs/resources.rst +++ b/docs/resources.rst @@ -1,6 +1,6 @@ -=============== -References -=============== +================ +Other resources +================ *Main resources including knowledge base and databases necessary for pipeline development* From 34675f28fc594f0b0b21ae15f527796b2bb72441 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Wed, 22 Jun 2022 22:56:51 +0200 Subject: [PATCH 11/15] fix space --- docs/index.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 7124a2512..e5355b71f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -25,7 +25,6 @@ bioinfo_softwares - .. toctree:: :caption: Development guide :name: development_guide @@ -37,4 +36,4 @@ README semver FAQs - resources + resources From 9190559716495774b0e07eeb54d3508490387a9d Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Thu, 23 Jun 2022 09:52:12 +0200 Subject: [PATCH 12/15] fix manta --- .../snakemake_rules/variant_calling/somatic_sv_tumor_only.rule | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule index db701f6c7..45914185c 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule @@ -19,7 +19,7 @@ rule manta_tumor_only: runmode = "local", tumor = get_sample_type(config["samples"], "tumor"), case_name = config["analysis"]["case_id"], - manta_install_path= "/opt/conda/share/manta-1.6.0-1" + manta_install_path= "/opt/conda/share/manta-1.6.0-2" threads: get_threads(cluster_config, "manta_tumor_only") message: From 51f2133a460aa1cd8ea9cb69d127cd6360ef5d8b Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Thu, 23 Jun 2022 10:03:47 +0200 Subject: [PATCH 13/15] fix manta --- .../variant_calling/somatic_sv_tumor_normal.rule | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule index e054a1f4f..e737bcd13 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule @@ -22,7 +22,7 @@ rule manta_tumor_normal: tumor = get_sample_type(config["samples"], "tumor"), normal = get_sample_type(config["samples"], "normal"), case_name = config["analysis"]["case_id"], - manta_install_path = "/opt/conda/share/manta-1.6.0-1" + manta_install_path = "/opt/conda/share/manta-1.6.0-2" threads: get_threads(cluster_config, "manta_tumor_normal") message: From f99bf80235c3c7f59e087aae76eb3fd135557280 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Thu, 23 Jun 2022 10:17:20 +0200 Subject: [PATCH 14/15] eaa --- CHANGELOG.rst | 2 +- docs/balsamic_filters.rst | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 76690aa1a..c323d858e 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -37,7 +37,7 @@ Fixed: * `run_validate.sh` script https://github.com/Clinical-Genomics/BALSAMIC/pull/952 * Somatic SV tumor normal rules https://github.com/Clinical-Genomics/BALSAMIC/pull/959 * Missing `genderChr` flag for `ascat_tumor_normal` rule https://github.com/Clinical-Genomics/BALSAMIC/pull/963 -* Command in vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966 +* Command in vcf2cytosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966 Removed ^^^^^^^ diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst index 089126ef5..b33780aa8 100644 --- a/docs/balsamic_filters.rst +++ b/docs/balsamic_filters.rst @@ -14,7 +14,7 @@ In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germ - Analysis type - Somatic/Germline - Variant type - * - DNAScope + * - DNAscope - WGS - tumor-normal, tumor-only - germline @@ -24,7 +24,7 @@ In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germ - tumor-normal, tumor-only - somatic - SNV, InDel - * - TNScope :superscript:`2` + * - TNscope :superscript:`2` - WGS - tumor-normal, tumor-only - somatic @@ -42,7 +42,7 @@ In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germ :superscript:`1` TNhaplotyper is only executed for tumor-only if a WGS case is being analysed -:superscript:`2` TNScope output is being merged with TNhaplotyper calls for TO-WGS analysis +:superscript:`2` TNscope output is being merged with TNhaplotyper calls for TO-WGS analysis From 0343a09d5c2db6c2d069b64cc89211ab4c184504 Mon Sep 17 00:00:00 2001 From: khurrammaqbool Date: Thu, 23 Jun 2022 10:26:00 +0200 Subject: [PATCH 15/15] aaaa --- docs/balsamic_sv_cnv.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/balsamic_sv_cnv.rst b/docs/balsamic_sv_cnv.rst index 2275f8d92..146bccf79 100644 --- a/docs/balsamic_sv_cnv.rst +++ b/docs/balsamic_sv_cnv.rst @@ -1,5 +1,5 @@ ************************************ -Structural and copy-number variants +Structural and Copy Number variants ************************************ Depending on the sequencing type, BALSAMIC is currently running the following structural and copy number variant callers: