Commit 72936783 authored by sajvanderzeeuw's avatar sajvanderzeeuw

Changes in documentation of GATK BASTY adn BastyGenerateFasta

parent 026b2015
......@@ -16,32 +16,44 @@ Biopet is build on top of GATK Queue, which requires having `java` installed on
For end-users:
* Java 7 JVM
* Minimum 2 GB RAM, more when analysis is also run on this machine.
* [Java 7 JVM](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [OpenJDK 7](http://openjdk.java.net/install/)
* [Cran R 3.1.1](http://cran.r-project.org/)
* [GATK](https://www.broadinstitute.org/gatk/download)
For developers:
* OpenJDK 7 or Oracle-Java JDK 7
* Minimum of 4 GB RAM {todo: provide more accurate estimation on building}
* [OpenJDK 7](http://openjdk.java.net/install/)
* [Cran R 3.1.1](http://cran.r-project.org/)
* Maven 3
* [Maven 3.2](http://maven.apache.org/download.cgi)
* [GATK + Queue](https://www.broadinstitute.org/gatk/download)
* IntelliJ or Netbeans 8.0 for development
* [IntelliJ](https://www.jetbrains.com/idea/) or [Netbeans > 8.0](https://netbeans.org/)
## How to use
### Running a pipeline
- Help: `java -jar Biopet(version).jar (pipeline of interest) -h`
- Local: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -run`
- Cluster: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub -jobParaEnv BWA -run`
- DryRun: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options)`
- DryRun (shark): `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub -jobParaEnv BWA`
- Help:
~~~
java -jar Biopet(version).jar (pipeline of interest) -h
~~~
- Local:
~~~
java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -run
~~~
- Cluster:
- Note that `-qsub` is cluster specific (SunGrid Engine)
~~~
java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub* -jobParaEnv YoureParallelEnv -run
~~~
- DryRun:
- A dry run can be performed to see if the scheduling and creating of the pipelines jobs performs well. Nothing will be executed only the job commands are created. If this succeeds it's a good indication you actual run will be successful as well.
- Each pipeline can be found as an options inside the jar file Biopet[version].jar which is located in the target directory and can be started with `java -jar <pipelineJarFile>`
~~~
java -jar Biopet(version).jar (pipeline of interest) (pipeline options)
~~~
### Shark Compute Cluster specific
In the SHARK compute cluster, a module is available to load the necessary dependencies.
......@@ -104,8 +116,6 @@ There are multiple configs that can be passed to a pipeline, for example the sam
- VcfToTsv
- WipeReads
## Developers
### Compiling Biopet
......@@ -117,10 +127,9 @@ There are multiple configs that can be passed to a pipeline, for example the sam
5. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
## About
Go to the [about page](about)
## License
See: [License](license)
See: [License](license.md)
By downloading the PROGRAM you agree to the following terms of use:
BROAD INSTITUTE
SOFTWARE LICENSE AGREEMENT
FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
1. DEFINITIONS
1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
2. LICENSE
2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
3. PHONE-HOME FEATURE
LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
4. OWNERSHIP OF INTELLECTUAL PROPERTY
LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
Copyright 2012-2014 Broad Institute, Inc.
Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
5. INDEMNIFICATION
LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
6. NO REPRESENTATIONS OR WARRANTIES
THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
7. ASSIGNMENT
This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
8. MISCELLANEOUS
8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
By downloading the PROGRAM you agree to the following terms of use:
BROAD INSTITUTE
SOFTWARE LICENSE AGREEMENT
FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
1. DEFINITIONS
1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
2. LICENSE
2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
3. PHONE-HOME FEATURE
LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
4. OWNERSHIP OF INTELLECTUAL PROPERTY
LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
Copyright 2012-2014 Broad Institute, Inc.
Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
5. INDEMNIFICATION
LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
6. NO REPRESENTATIONS OR WARRANTIES
THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
7. ASSIGNMENT
This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
8. MISCELLANEOUS
8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
Copyright (c) 2012 The Broad Institute
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Copyright [2013-2014] [Sequence Analysis Support Core](https://sasc.lumc.nl/)
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
......@@ -3,7 +3,7 @@
## Introduction
The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
It uses the <a href="https://www.broadinstitute.org/gatk/guide/best-practices" target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
It is based on the <a href="https://www.broadinstitute.org/gatk/guide/best-practices" target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
The pipeline accepts ```.fastq & .bam``` files as input.
## Tools for this pipeline
......@@ -46,16 +46,69 @@ To run the pipeline:
~~~
java -jar Biopet.0.2.0.jar pipeline gatkPipeline -run -config MySamples.json -config MySettings.json -outDir myOutDir
~~~
For LUMC/researchSHARK users there is a module available that sets all your environment settings and default executables/settings.
To check if your pipeline can create all the jobs (dry run) remove the `-run`:
~~~
module load Biopet/0.2.0
biopet pipeline gatkPipeline -run -config MySamples.json -config MySettings.json -outDir myOutDir
java -jar Biopet.0.2.0.jar pipeline gatkPipeline -config MySamples.json -config MySettings.json -outDir myOutDir
~~~
## Examine results
## Results
### Result files
~~~
.
└── samples
├── my_sample1
│   ├── run_lib1
│   │   ├── chunks
│   │   │   ├── 1
│   │   │      └── flexiprep
│   │   │
│   │   │
│   │   │
│   │   ├── flexiprep
│   │   │   ├── input.R1.fastqc
│   │   │   │   └── input.R1_fastqc
│   │   │   │   ├── Icons
│   │   │   │   └── Images
│   │   │   ├── input.R1.qc.fastqc
│   │   │   │   └── input.R1.qc_fastqc
│   │   │   │   ├── Icons
│   │   │   │   └── Images
│   │   │   ├── input.R2.fastqc
│   │   │   │   └── input.R2_fastqc
│   │   │   │   ├── Icons
│   │   │   │   └── Images
│   │   │   └── input.R2.qc.fastqc
│   │   │   └── input.R2.qc_fastqc
│   │   │   ├── Icons
│   │   │   └── Images
│   │   └── metrics
│   ├── run_lib2
│   │   ├── chunks
│   │   │   ├── 1
│   │   │   └── flexiprep
│   │   │
│   │   ├── flexiprep
│   │   │   ├── input.R1.fastqc
│   │   │   │   └── input.R1_fastqc
│   │   │   │   ├── Icons
│   │   │   │   └── Images
│   │   │   ├── input.R1.qc.fastqc
│   │   │   │   └── input.R1.qc_fastqc
│   │   │   │   ├── Icons
│   │   │   │   └── Images
│   │   │   ├── input.R2.fastqc
│   │   │   │   └── input.R2_fastqc
│   │   │   │   ├── Icons
│   │   │   │   └── Images
│   │   │   └── input.R2.qc.fastqc
│   │   │   └── input.R2.qc_fastqc
│   │   │   ├── Icons
│   │   │   └── Images
│   │   └── metrics
│   └── variantcalling
~~~
### Best practice
......
......@@ -10,15 +10,19 @@ Which makes it very easy to look at the variations between certain species or st
* <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>
## Example
To run for a specific species, please do not forget to create the proper index files:
## Requirements
To run for a specific species, please do not forget to create the proper index files.
The index files are created from the supplied reference:
* ```.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)
For the help screen:
## Example
#### For the help screen:
~~~
java -jar Biopet.0.2.0.jar pipeline basty -h
~~~
......@@ -30,14 +34,6 @@ Note that one should first create the appropriate [configs](../config.md).
java -jar Biopet.0.2.0.jar pipeline basty -run -config MySamples.json -config MySettings.json -outDir myOutDir
~~~
For LUMC/researchSHARK users there is a module available that sets all your environment settings and default executables/settings.
~~~
module load Biopet/0.2.0
biopet pipeline basty -run -config MySamples.json -config MySettings.json -outDir myOutDir
~~~
## Result files
The output files this pipeline produces are:
......
......@@ -57,25 +57,6 @@ java -jar Biopet-0.2.0.jar tool BastyGenerateFasta --inputVcf myVCF.vcf --bamFil
--outputName NiceTool --outputConsensusVariants myConsensusVariants.fasta
~~~
For LUMC/researchSHARK users there is a module available that sets all your environment settings and default executables/settings.
~~~
module load Biopet/0.2.0
# Minimal example for option: outputVariants (VCF based)
biopet tool BastyGenerateFasta --inputVcf myVCF.vcf \
--outputName NiceTool --outputVariants myVariants.fasta
# Minimal example for option: outputConsensus (BAM based)
biopet tool BastyGenerateFasta --bamFile myBam.bam \
--outputName NiceTool --outputConsensus myConsensus.fasta
# Minimal example for option: outputConsensusVariants
biopet tool BastyGenerateFasta --inputVcf myVCF.vcf --bamFile myBam.bam \
--outputName NiceTool --outputConsensusVariants myConsensusVariants.fasta
~~~
## Output
* FASTA containing variants only
......
......@@ -2,13 +2,11 @@ site_name: Biopet user manual
pages:
- ['index.md', 'Home']
- ['config.md', 'Config']
- ['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']
- ['pipelines/basty.md', 'Pipelines', 'Basty']
- ['pipelines/GATK-pipeline.md', 'Pipelines', 'GATK-pipeline']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
- ['pipelines/sage.md', 'Pipelines', 'Sage']
- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
- ['cluster/oge.md', 'OpenGridEngine']
......
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