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MIP performs whole genome or target region analysis of sequenced single-end and/or paired-end reads from the Illumina plattform in fastq\(.gz\) format to generate annotated ranked potential disease causing variants.
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MIP performs whole genome or target region analysis of sequenced single-end and/or paired-end reads from the Illumina platform in fastq\(.gz\) format to generate annotated ranked potential disease causing variants.
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MIP performs QC, alignment, coverage analysis, variant discovery and annotation, sample checks as well as ranking the found variants according to disease potential with a minimum of manual intervention. MIP is compatible with Scout for visualization of identified variants. MIP analyses snv, indels and SV.
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MIP has been in use in the clinical production at the Clinical Genomics facility at Science for Life Laboratory since 2014.
We recommend perlbrew for installing and managing perl and cpanm libraries. Installation instructions and setting up specific cpanm libraries can be found [here](https://github.com/Clinical-Genomics/development/blob/master/perl/installation/installation.md).
- Some versions of the cpan module List::MoreUtils has conflicts with certain versions of Perl. Perl v 5.18.2 has been confirmed to be compatible with version 0.4.13 of the List::MoreUtils module.
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If you experience issues with that module, try to reinstall it by running: ``cpanm --reinstall List::[email protected]``
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##### 3.Test conda and mip_installation (optional)
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```Bash
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$ cd t; prove mip_install.t
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$ cd -
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```
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2.Create the install instructions for MIP
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```
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##### 4.Create the install instructions for MIP
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```Bash
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$ perl mip_install.pl
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```
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This will generate a batch script "mip.sh" for the install in your working directory. Use ``--help`` to see
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parameters that can be used in the installation process.
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#### *Conda*
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You can decide to install in the conda default environment or use a conda environment with ``--env [env_name]``.
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If you have installed conda in another location than the default you have to supply the path to the location
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using ``--conda_dir_path [conda_directory_path]``.
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#### *Perl*
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MIP requires perl version (>=5.18) and the installation process will upgrade the perl version to at least 5.18 for the user
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if you enable ``--perl_install``. Cpanm will be installed if you install a new perl version and used to download required
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perl modules. Currently MIP does not use the conda perl installation, but installs perl and cpanm outside of conda.
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##### *NOTE*
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This will add the following lines to bashrc and bash_profile if the install perl version is not found in your path:
MIP requires many references depending on what modules in MIP you decide to run. MIP ships with a download script
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that will attempt to download references that are available in public repositories. This feature can be enables with
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by supplying a ``--reference_dir [reference_dir]`` in the installation process.
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##### *NOTE*
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Some references are quite large and will take time to download. You might want to run this using screen or tmux.
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3. Run the bash script
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```
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This will generate a batch script "mip.sh" for the install in your working directory.
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###### *Note:*
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- The batch script will install the MIP dependencies in Conda's root environment. Often it is beneficial to create a separate environment for each of your applications. In order to create a separate environment for MIP supply the ``-env [env_name]`` flag when running *mip_install.pl*.
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- There is currently an issue with installing GATK via Conda causing the installation process to freeze. The solution at the moment is to turn of the GATK installation by running the install script together with the ``-skip gatk`` flag and install [GATK] manually.
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- For a full list of available options and parameters, run: ``$ perl mip_install.pl --help``
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- For a full list of parameter defaults, run: ``$ perl mip_install.pl -ppd``
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##### 5.Run the bash script
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```Bash
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$ bash mip.sh
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```
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This will install all the dependencies of MIP and other modules included in MIP into a conda environment.
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However a fresh version of perl and cpanm is installed, if enabled, outside of the conda environment, but are activated through bashrc and bash_profile.
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#### *Optional*
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Make sure to activate your conda environment if that option was used above.
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Test Perl modules and MIP
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```
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$ cd t; prove run_tests.t
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This will install MIP and most of its dependencies into a conda environment.
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###### *Note:*
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- Some references are quite large and will take time to download. You might want to run this using screen or tmux.
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##### 6.Test your MIP installation (optional)
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Make sure to activate your conda environment if that option was used above.
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```Bash
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$ cd t; prove -r
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$ cd -
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```
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##### 7.Install tools with conflicting dependencies
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Tools that have conflicting dependencies needs to be installed in separate conda environments. Currently these programs requires separate environments:
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4. Run MIP
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* Genmod, Chanjo, Multiqc and Variant_integrity
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- requires python 3
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* Peddy
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- conflicts with SVDB dependencies
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* CNVnator
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- Requires access to ROOT which disturbs the normal linking of C libraries
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*Conda default environment*
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```
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$ mip
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```
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*Conda environment*
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```
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$ source activate conda_env
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$ mip
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```
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### Prerequisites
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##### Programs/Modules
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* Perl modules: There are several perl modules that are used by MIP which are not included in the Perl standard distribution. These need to be downloaded from [CPAN]. The install script will attempt to download all required perl modules and you can also list them and programs using ``perl mip_install -ppd``.
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* Simple Linux Utility for Resource Management \(SLURM\)
In your config yaml file or on the command line you will have to supply the ``module_source_environment_command`` parameter to activate the conda environment specific for the tool. Here is an example with three Python 3 tools in their own environment and Peddy and VEP and CNVnator in each own, with some extra initialization:
MIP will execute this on the node before executing the program and then revert to the ``--source_main_environment_command`` if set. Otherwise ``source deactivate`` is used to return to the conda root environment.
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### Usage
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MIP is called from the command line and takes input from the command line \(precedence\ or falls back on defaults where applicable.
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MIP is called from the command line and takes input from the command line \(precedence\) or falls back on defaults where applicable.
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Lists are supplied as repeated flag entries on the command line or in the config using the yaml format for arrays.
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Only flags that will actually be used needs to be specified and MIP will check that all required parameters are set before submitting to SLURM.
@@ -209,18 +207,24 @@ Program parameters always begins with "p" followed by a capital letter. Program
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MIP will overwrite data files when reanalyzing, but keeps all "versioned" sbatch scripts for traceability.
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You can always supply `perl mip.pl -h` to list all availaible parameters and defaults.
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You can always supply `perl mip.pl --help` to list all available parameters and defaults.
This will analyse family 3 using 3 individuals from that family and begin the analysis with programs after Bwa mem and use all parameter values as specified in the config file except those supplied on the command line, which has precedence.
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#### Input
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All references and template files should be placed directly in the reference directory specified by `--reference_dir`, except for ANNOVAR db files, which should be located in annovar/humandb.
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All references and template files should be placed directly in the reference directory specified by `--reference_dir`.
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##### Meta-Data
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* [Pedigree file] \(YAML-format\)
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* [Configuration file] \(YAML-format\)
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#### Output
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@@ -236,5 +240,7 @@ MIP will place any generated datafiles in the output data directory specified by
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