Commit 4b60e366 authored by sajvanderzeeuw's avatar sajvanderzeeuw

Changes in docs

parent eb74d901
......@@ -9,6 +9,7 @@ The sample config should be in [__JSON__](http://www.json.org/) format
- Third field contains __"R1" or "R2"__ or __"bam"__
- The fastq input files can be provided zipped and un zipped
#### Example sample config
~~~
{
"samples":{
......@@ -48,4 +49,50 @@ Note that there is a tool called [SamplesTsvToJson](tools/SamplesTsvToJson.md) t
### The settings config
The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
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The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
This config file should be written in JSON format. It can contain setup settings like references for the tools used,
if the pipeline should use chunking or setting memory limits for certain programs almost everything can be adjusted trough this config file.
One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer deeper into the JSON file.
E.g. in the example below the settings for Picard tools are altered only for Picard and not global.
~~~
"picard": { "validationstringency": "LENIENT" }
~~~
Global setting examples are:
~~~
"java_gc_timelimit": 98,
"numberchunks": 25,
"chunking": true
~~~
----
#### Example settings config
~~~
{
"reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
"dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
"joint_variantcalling": false,
"haplotypecaller": { "scattercount": 100 },
"multisample": { "haplotypecaller": { "scattercount": 1000 } },
"picard": { "validationstringency": "LENIENT" },
"library_variantcalling_temp": true,
"target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
"min_dp": 5,
"bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
"bam_to_fastq": true,
"baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
"samtofastq": {"memory_limit": 8, "vmem": "16G"},
"java_gc_timelimit": 98,
"numberchunks": 25,
"chunking": true,
"haplotypecaller": { "scattercount": 1000 }
}
~~~
### JSON validation
To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file
# Introduction
## [Basty](https://git.lumc.nl/biopet/biopet/tree/develop/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty)
A pipeline for aligning bacterial genomes and detect structural variations on the level of SNPs. Basty will output phylogenetic trees.
Which makes it very easy to look at the variations between certain species.
# Tools
* GATK-pipeline []()
* FASTA builder [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
* RAxml []()
* Gubbins []()
# Invocation
# Example
......
# Introduction
# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/master/flexiprep)
# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/develop/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep)
QC pipeline for fastq files
......
......@@ -2,13 +2,14 @@ site_name: Biopet user manual
pages:
- ['index.md', 'Home']
- ['config.md', 'Config']
- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['pipelines/basty.md', 'Pipelines', 'Basty']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
- ['pipelines/sage.md', 'Pipelines', 'Sage']
- ['pipelines/yamsvp.md', 'Pipelines', 'Yamsvp']
- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
- ['cluster/oge.md', 'OpenGridEngine']
- ['about.md', 'About']
- ['license.md', 'License']
......
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