Merge pull request #1183 from FriederikeHanssen/docs

nf-core · Aug 17, 2023 · 721c8d1 · 721c8d1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1173](https://github.com/nf-core/sarek/pull/1173) - Fixed duplicated entries in joint germline recalibrated VCF ([#966](https://github.com/nf-core/sarek/pull/966), [#1102](https://github.com/nf-core/sarek/pull/1102)),
   fixed grouping joint germline recalibrated VCF ([#1137](https://github.com/nf-core/sarek/pull/1137))
 - [#1177](https://github.com/nf-core/sarek/pull/1177) - Fix status inference when using nf-validation plugin
+- [#1183](https://github.com/nf-core/sarek/pull/1183) - Add docs for concatentated germline variants
 
 ### Dependencies
 

diff --git a/README.md b/README.md
@@ -123,13 +123,19 @@ We thank the following people for their extensive assistance in the development
 - [Adam Talbot](https://github.com/adamrtalbot)
 - [Adrian Lärkeryd](https://github.com/adrlar)
 - [Alexander Peltzer](https://github.com/apeltzer)
+- [Alison Meynert](https://github.com/ameynert)
 - [Anders Sune Pedersen](https://github.com/asp8200)
+- [arontommi](https://github.com/arontommi)
+- [BarryDigby](https://github.com/BarryDigby)
 - [Bekir Ergüner](https://github.com/berguner)
+- [bjornnystedt](https://github.com/bjornnystedt)
+- [cgpu](https://github.com/cgpu)
 - [Chela James](https://github.com/chelauk)
 - [David Mas-Ponte](https://github.com/davidmasp)
 - [Francesco Lescai](https://github.com/lescai)
 - [Gavin Mackenzie](https://github.com/GCJMackenzie)
 - [Gisela Gabernet](https://github.com/ggabernet)
+- [gulfshores](https://github.com/gulfshores)
 - [Harshil Patel](https://github.com/drpatelh)
 - [James A. Fellows Yates](https://github.com/jfy133)
 - [Jesper Eisfeldt](https://github.com/J35P312)
@@ -144,6 +150,7 @@ We thank the following people for their extensive assistance in the development
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)
+- [pallolason](https://github.com/pallolason)
 - [Paul Cantalupo](https://github.com/pcantalupo)
 - [Phil Ewels](https://github.com/ewels)
 - [Sabrina Krakau](https://github.com/skrakau)
@@ -154,13 +161,6 @@ We thank the following people for their extensive assistance in the development
 - [Szilveszter Juhos](https://github.com/szilvajuhos)
 - [Tobias Koch](https://github.com/KochTobi)
 - [Winni Kretzschmar](https://github.com/winni2k)
-- [arontommi](https://github.com/arontommi)
-- [BarryDigby](https://github.com/BarryDigby)
-- [bjornnystedt](https://github.com/bjornnystedt)
-- [cgpu](https://github.com/cgpu)
-- [gulfshores](https://github.com/gulfshores)
-- [pallolason](https://github.com/pallolason)
-- [Alison Meynert](https://github.com/ameynert)
 
 ## Acknowledgements
 

diff --git a/docs/output.md b/docs/output.md
@@ -44,6 +44,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - [Control-FREEC](#control-freec)
   - [MSI status](#msi-status)
     - [MSIsensorPro](#msisensorpro)
+  - [Concatenation](#concatentation)
 - [Variant annotation](#variant-annotation)
   - [snpEff](#snpeff)
   - [VEP](#vep)
@@ -759,6 +760,20 @@ It requires a normal sample for each tumour to differentiate the somatic and ger
   - Germline sites detected.
   </details>
 
+### Concatentation
+
+Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, `Manta`, `bcftools mpileup`, `Strelka2`, or `Tiddit` are concatenated with `bcftools concat`. The field `SOURCE` is added to the VCF header to report the variant caller.
+
+<details markdown="1">
+<summary>Concatenated VCF-files for normal samples</summary>
+
+**Output directory: `{outdir}/variantcalling/concat/<sample>/`**
+
+- `<sample>.germline.vcf.gz` and `<sample>.germline.vcf.gz.tbi`
+  - VCF with tabix index
+
+</details>
+
 ## Variant annotation
 
 This directory contains results from the final annotation steps: two tools are used for annotation, [snpEff](http://snpeff.sourceforge.net/) and [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html). Both results can also be combined by setting `--tools merge`.

diff --git a/docs/usage.md b/docs/usage.md
@@ -308,40 +308,6 @@ test,sample4_vs_sample3,manta,sample4_vs_sample3.diploid_sv.vcf.gz
 test,sample4_vs_sample3,manta,sample4_vs_sample3.somatic_sv.vcf.gz
 ```
 
-## Sentieon
-
-[Sentieon](https://www.sentieon.com/) is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional high accuracy, and 100% consistency.
-
-In particular, Sentieon contains what may be view as speedup version of some standard GATK tools, like bwamem and haplotyper. Sarek contains support for some of the functions in Sentieon. In order to use those functions, the user will need to supply Sarek with a license for Sentieon.
-
-### Setup of Sentieon license
-
-Sentieon supply license in the form of a string-value (a url) or a file. It should be base64-encoded and stored in a nextflow secret named `SENTIEON_LICENSE_BASE64`. If a license string (url) is supplied, then the nextflow secret should be set like this:
-
-```bash
-nextflow secret set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
-```
-
-If a license file is supplied, then the nextflow secret should be set like this:
-
-```bash
-nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-```
-
-### Available Sentieon functions
-
-Sarek contains the following Sentieon functions [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.
-
-### Basic usage of Sentieon functions
-
-To use Sentieon's aligner `bwa mem`, set the aligner option `sentieon-bwamem`. (This can, for example, be done by adding `--aligner sentieon-bwamem` to the nextflow run command.)
-
-To use Sentieon's function `Dedup`, specify `sentieon_dedup` as one of the tools. (This can, for example, be done by adding `--tools sentieon_dedup` to the nextflow run command.)
-
-To use Sentieon's function `Haplotyper`, specify `sentieon_haplotyper` as one of the tools. This can, for example, be done by adding `--tools sentieon_haplotyper` to the nextflow run command. In order to skip the GATK-based variant-filter, one may add `--skip_tools haplotyper_filter` to the nextflow run command. Sarek also provides the option `sentieon_haplotyper_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) of Sentieon's haplotyper. Sentieon's haplotyper can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_haplotyper_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.
-
-To use Sentieon's function `GVCFtyper` along with Sention's version of VQSR (`VarCal` and `ApplyVarCal`) for joint-germline genotyping, specify `sentieon_haplotyper` as one of the tools, set the option `sentieon_haplotyper_emit_mode` to `gvcf`, and add the option `joint_germline`. This can, for example, be done by adding `--tools sentieon_haplotyper --joint_germline --sentieon_haplotyper_emit_mode gvcf` to the nextflow run command.
-
 ## Updating the pipeline
 
 When you launch a pipeline from the command-line with `nextflow run nf-core/sarek -profile docker -params-file params.yaml`, Nextflow will automatically pull the pipeline code from GitHub and store it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
@@ -1041,6 +1007,38 @@ ERROR_CHROMOSOME_NOT_FOUND      17522411
 
 ## Sentieon
 
+[Sentieon](https://www.sentieon.com/) is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional high accuracy, and 100% consistency.
+
+In particular, Sentieon contains what may be view as speedup version of some standard GATK tools, like bwamem and haplotyper. Sarek contains support for some of the functions in Sentieon. In order to use those functions, the user will need to supply Sarek with a license for Sentieon.
+
+### Setup of Sentieon license
+
+Sentieon supply license in the form of a string-value (a url) or a file. It should be base64-encoded and stored in a nextflow secret named `SENTIEON_LICENSE_BASE64`. If a license string (url) is supplied, then the nextflow secret should be set like this:
+
+```bash
+nextflow secret set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
+```
+
+If a license file is supplied, then the nextflow secret should be set like this:
+
+```bash
+nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
+```
+
+### Available Sentieon functions
+
+Sarek contains the following Sentieon functions [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.
+
+### Basic usage of Sentieon functions
+
+To use Sentieon's aligner `bwa mem`, set the aligner option `sentieon-bwamem`. (This can, for example, be done by adding `--aligner sentieon-bwamem` to the nextflow run command.)
+
+To use Sentieon's function `Dedup`, specify `sentieon_dedup` as one of the tools. (This can, for example, be done by adding `--tools sentieon_dedup` to the nextflow run command.)
+
+To use Sentieon's function `Haplotyper`, specify `sentieon_haplotyper` as one of the tools. This can, for example, be done by adding `--tools sentieon_haplotyper` to the nextflow run command. In order to skip the GATK-based variant-filter, one may add `--skip_tools haplotyper_filter` to the nextflow run command. Sarek also provides the option `sentieon_haplotyper_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) of Sentieon's haplotyper. Sentieon's haplotyper can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_haplotyper_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.
+
+To use Sentieon's function `GVCFtyper` along with Sention's version of VQSR (`VarCal` and `ApplyVarCal`) for joint-germline genotyping, specify `sentieon_haplotyper` as one of the tools, set the option `sentieon_haplotyper_emit_mode` to `gvcf`, and add the option `joint_germline`. This can, for example, be done by adding `--tools sentieon_haplotyper --joint_germline --sentieon_haplotyper_emit_mode gvcf` to the nextflow run command.
+
 ### Joint germline variant calling
 
 Sentieon's [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) does not support the [GenomicsDB](https://gatk.broadinstitute.org/hc/en-us/articles/5358869876891-GenomicsDBImport) datastore format. This means that, in contrast to the GATK based joint germline variant calling subworkflow in Sarek, the Sentieon/DNAseq based joint germline variant calling subworkflow does not use the GenomicsDB datastore format.