Commit 7c333019 authored by bow's avatar bow
Browse files

Merge branch 'docs_v.0.3.0' into release-0.3.0

parents 635feee0 0d45a06f
......@@ -12,7 +12,7 @@ Biopet is an abbreviation of ( Bio Pipeline Execution Tool ) and packages severa
### System Requirements
Biopet is build on top of GATK Queue, which requires having `java` installed on the analysis machine(s).
Biopet is build on top of GATK Queue, which requires having `java 7 JVM` installed on the analysis machine(s).
For end-users:
......@@ -58,7 +58,7 @@ If one performs a dry run the config report will be generated. From this config
In the SHARK compute cluster, a module is available to load the necessary dependencies.
$ module load biopet/v0.2.0
$ module load biopet/v0.3.0
Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biopet` can be started using:
......@@ -70,25 +70,32 @@ Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biop
$ biopet pipeline <pipeline_name>
- [Flexiprep](pipelines/flexiprep)
- [Mapping](pipelines/mapping)
- [Gatk Variantcalling](https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline)
- [Gentrap](pipelines/gentrap)
- [Sage](pipelines/sage)
- Bam2Wig
- BamMetrics
- Carp
- ConiferPipeline
- Toucan
- Yamsvp
- Basty
Note that all pipelines are still in the experimental phase and therefore one needs to be careful interpreting the results and stability of the pipelines
- GatkBenchmarkGenotyping
- GatkGenotyping
- GatkPipeline
- GatkVariantRecalibration
- GatkVcfSampleCompare
- [Gentrap](pipelines/gentrap)
- [Sage](pipelines/sage)
- Yamsvp (Under development)
__Note that each pipeline needs a config file written in JSON format see [config](general/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.
There are multiple configs that can be passed to a pipeline, for example the sample, settings and executables where from sample and settings are mandatory.
- [Here](general/config.md) one can find how to create a sample and settings config
- More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
......@@ -97,20 +104,33 @@ There are multiple configs that can be passed to a pipeline, for example the sam
$ biopet tool <tool_name>
- BedToInterval
- BedtoolsCoverageToCounts
- BiopetFlagstat
- CheckAllelesVcfInBam
- ExtractAlignedFastq
- FastqSplitter
- FindRepeatsPacBio
- MpileupToVcf
- SageCountFastq
- SageCreateLibrary
- SageCreateTagCounts
- VcfFilter
- VcfToTsv
- WipeReads
- AnnotateVcfWithBed
- BastyGenerateFasta
- BedToInterval
- BedtoolsCoverageToCounts
- BiopetFlagstat
- CheckAllelesVcfInBam
- ExtractAlignedFastq
- FastqSplitter
- FastqSync
- FindRepeatsPacBio
- MergeAlleles
- MpileupToVcf
- SageCountFastq
- SageCreateLibrary
- SageCreateTagCounts
- SamplesTsvToJson
- Seqstat
- VEPNormalizer
- VcfFilter
- VcfStats
- VcfToTsv
- WipeReads
Each tool has its own help screen and can be accessed like this:
$ biopet tool <tool_name> -h
## Developers
......@@ -122,8 +142,7 @@ There are multiple configs that can be passed to a pipeline, for example the sam
4. alternatively download the `queue.jar` from the GATK website
5. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
## About
## About
Go to the [about page](about)
## License
......
# Release notes BioPet version 0.3.0
Since our first release in December 2014 many new functions have been added to the pipelines including:
- Multisample compatibility
- Copy number analysis
- Structural variants analysis
- Full RNA-seq pipeline
- Annotation pipeline ( still under development )
- Summary framework
- Md5sum of all input/output files ( need to be provided in the summary )
- Sequence stats
- Program stats/versions
- mapping stats
- Tool stats ( if pipeline uses a biopet tool, it will output the version of the tool and all other statistics that might be captured )
- GATK variantcalling has a lot of new features and is now called SHIVA
- A entire new pipeline named Gentrap based on our previous [Makefile version](http://sasc-server.lumcnet.prod.intern/pipelines/makefile-0.6.0/gentrap/), with extra features like:
- remove all ribosomal reads
- a tool for building the correct annotation for read.counting etc etc.
Also a impressive list of tools have been added to the updated framework:
- AnnotateVcfWithBed ( This enables the user to Annotate a VCF file based on a bed file containing the locations of interest )
- CheckAllelesVcfInBam
- ExtractAlignedFastq
- FastqSplitter
- FastqSync
- SamplesTsvToJson
- Seqstat ( this is a lift over tool based on our previous python implementation of seqstat )
- VEPNormalizer ( This normalizer enables a user to parse VEP output VCFs to the exact specs of [VCF 4.1](https://samtools.github.io/hts-specs/VCFv4.1.pdf) )
- VcfStats
Some tools have a new version for better compatibility with our latest pipelines. The tools that have a changed version are:
- FastQC v0.11.2
- seqTK Version: 1.0-r63-dirty
- sickle version 1.33
- Cutadapt 1.5
- GSNAP version 2014-12-22
- TopHat v2.0.13
- cufflinks v2.2.1
- HTseq-count version 0.6.1p1
- pdfTeX, Version 3.1415926-2.5-1.40.14 (pdflatex)
- R scripting front-end version 3.1.1 (2014-07-10) (Rscript)
- tabix Version: 0.2.5 (r1005)
- grep (GNU grep) 2.16
- gzip 1.6
- Samtools Version: 1.1
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