Commit 1c537b84 authored by sajvanderzeeuw's avatar sajvanderzeeuw

Changes in docs

parent 0613bc7e
......@@ -73,7 +73,7 @@ Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biop
- [Sage](pipelines/sage)
- Yamsvp (Under development)
__Note that each pipeline needs a config file written in JSON format see [config](config) & [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config) __
__Note that each pipeline needs a config file written in JSON format see [config](config.md) & [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config) __
There are multiple configs that can be passed to a pipeline, for example the sample, settings and executables wherefrom sample and settings are mandatory.
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# Introduction
## [Basty](https://git.lumc.nl/biopet/biopet/tree/develop/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty)
## <a href="https://git.lumc.nl/biopet/biopet/tree/develop/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty" target="_blank">Basty</a>
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 []()
# Tools for this pipeline
* [GATK-pipeline](GATK-pipeline.md)
* [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
* <a href="http://sco.h-its.org/exelixis/software.html" target="_blank">RAxml</a>
* <a href="https://github.com/sanger-pathogens/Gubbins" target="_blank">Gubbins</a>
# Invocation
~~~
java -jar Biopet.0.2.0.jar pipeline basty
~~~
# Example
To run for a specific species, please do not forget to create the proper index files:
* ```.dict``` (can be produced with <a href="http://broadinstitute.github.io/picard/" target="_blank">Picard tool suite</a>)
* ```.fai``` (can be produced with <a href="http://samtools.sourceforge.net/samtools.shtml" target="_blank">Samtools faidx</a>
* ```.idxSpecificForAligner``` (depending on which aligner is used one should create a suitable index specific for that aligner.
Each aligner has his own way of creating index files. Therefore the options for creating the index files can be found inside the aligner itself)
# Testcase A
# Testcase B
# Examine results
## Result files
The output files this pipeline produces are:
* A complete output from [Flexiprep](flexiprep.md)
* BAM files, produced with the mapping pipeline. (either BWA, Bowtie, Stampy, Star and Star 2-pass. default: BWA)
* VCF file from all samples together
* The output from the tool [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
* FASTA containing variants only
* FASTA containing all the consensus sequences based on min. coverage (default:8) but can be modified in the config
* A phylogenetic tree based on the variants called with the GATK-pipeline generated with the tool [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
## Best practice
# References
......@@ -2,12 +2,13 @@ site_name: Biopet user manual
pages:
- ['index.md', 'Home']
- ['config.md', 'Config']
- ['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']
- ['pipelines/basty.md', 'pipelines', 'Basty']
- ['pipelines/GATK-pipeline.md', 'pipelines', 'GATK-pipeline']
- ['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']
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