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Updated to MIP version 3.0
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@henrikstranneheim
henrikstranneheim committed Jun 8, 2016
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2 changes: 2 additions & 0 deletions docs/MIP_overview.rst
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Expand Up @@ -44,6 +44,7 @@ Features
* Analyses a X-ten sequenced genome in approximately 21 h
* Rapid mode analyzes a WGS sample in approximately 4 h using a data reduction and parallelization scheme
- Traceability
* Track the status of each modules through dynamically updated status logs
* Recreate your analysis from the MIP log or generated config files
* Logs sample meta-data and sequence meta-data
* Logs version numbers of softwares and databases
Expand All @@ -56,6 +57,7 @@ Features
* Separate pathogenic transcripts for correct downstream annotation
* Annotate all alleles for a position
* Split multi-allelic records into single records to ease annotation
* Left align and trim variants to normalise them prior to annotation
* Annotate coverage across genetic region using Chanjo
* Extracts QC-metrics and stores them in YAML format
- Standardized
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89 changes: 89 additions & 0 deletions docs/change_log.rst
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@@ -1,6 +1,95 @@
Change Log
===========

MIP v2.6 --> v3.0

- Added Net/SSLeay.pm to install.pl
- Added option to skip perl install
- Added Manta, Delly, FT and CNVnator as structural variant callers
- Added modules CombineStructuralVariants, SVVariantEffectPredictor, SVVCFParser, SVRanking
- Added merging of samples in “other” chains to family chain for parallel modules
- Added CNVnator version. Had to be done at start up since CNVnator does not add its version to the output.
- Added Delly version on sample level
- Added Manta version on sample level
- Added SVVEP version and cache version
- Fixed bug causing VEP version to be lost for snvs/indels
- Added SVVCFParser version
- Added SVGenmod/rankModel version
- Added test for GATKCombineVariantsPrioritizeCaller to not include turned of variant callers
- Added snpEff download of reference genome to avoid race conditions
- Fixed python virtuelenvironment to not check programs if uve = 0
- Added VEP/SVVEP assembly, gencode, gene build, HGMDPublic, polyphen, regbuild, Sift, version to qcmetrics
- made NIST ID settable
- Removed PicardMergeSwitch, now all files are merged or renamed (single files) for more consequent naming and easier processing
- Renamed ‘fileEnding’ to ‘fileTag’ and ‘removefileEnding’ to ‘fileEnding’
- Change name of BAMCalibrationAndGTBlock to only BAMCalibrationBlock
- List::Util is in core module perl 5.18 replaces List::MoreUtils
- Use say instead of print where relevant
- Use internal Perl system commands instead of UNIX (copy, make_path)
- Removed mip log file if present in config to avoid appending to old log file. Supply on log file on cmd if you want to append to log file.
- Added plink2 installation via bioconda in install script
- Changed binary i MIP from plink to plink2
- Added MultiQC in install script and as MIP module
- Changed samtools stats module to include complete report for MultiQC processing
- Made pPicardToolsMergeSamFiles mandatory: Always run even for single samples to rename them correctly for standardised downstream processing. Will also split alignment per contig and copy to temporary directory for '-rio 1' block to enable selective removal of block submodules.
- Added LOFTEE VEP plugin: https://github.com/konradjk/loftee
- Added LofTool VEP plugin
- Added Modern::Perl ‘2014’
- Added PERL_UNICODE=SAD to install script, and hence bash_profile - stdin, stdout, and stderr to UTF‑8 as well as @ARGV and data handlers
- Use UTF-8 for all source script
- Added encoding UTF-8 pragma for open to default expect unicode when opening and writing
- Enforce perl 5.18 version
- Added autodie for generalised error and exception handling
- Removed dateTime and use less cumbersome core module Time::Piece
- Removed DV and added AD for samtools mpileup
- Added joint calling of SV using Manta
- Added SV analysis of exomes using Manta
- Modified CombineSVVariants to use Delly and CNVnator on sample-level and Manta on family level
- Added bcf generation of ranked vcf both select file and research
- Fixed bug in temp directory
- Bumped install version to 3.5.1
- Added Genmod temp dir flag
- Added sacct commands to trap for each sbatch to relay progress to MIP log file.status
- Made Sacct dependency into afterany
- Added pPrepareForVariantAnnotationBlock
- Removed pythonVirtualEnv and commands as conda is prefered
- Added sourceEnvironmentCommand
- Added '-pp' and '-ppm'
- Add bcf conversion of select and research variants to MIP
- Added check of programs mode to allowed values, more strict parsing for flaggs expecting numbers
- Select variants prior to Plink processing using GATK Select variants
- Move processing to node, but keept final output printing to hds
- Added SV annotation using 1000G SV and vcfanno -ends
- Added vcfanno, lua, config
- Annotate from 1000G SV
- Modified svrank_mdodel to take 1000G frequency in account
- Add vcfanno version in SVCombineVariantCallSets
- Updated fastqc to version 0.11.5
- Updated bwa to version 0.7.13
- Updated sambamba to version 0.6.1
- Added “—fix-mate-overlaps” to avoid counting overlapping reads twice
- Removed Sambamba version from MIP flagg
- Updated picardtools to version 2.3.0
- Updated Chanjo to version 3.4.1
- Updated Manta to version 0.29.6
- Updated Genmod to version 3.5.2
- Updated MultiQC to version 0.6
- Updated Vip to version 84
- Added Picardtools Markduplicates as a option and default
- Added more SambambaMarkDup options
- Make sambamba flagstats into subroutine to be used for all markdup
- Remade capture kit options into 1 hash flag, which will build all associated files if 1 is lacking
- Make Covariates to be used in the recalibration in GATKBASERCAL to be flag and array option
- annotations, -Know and -knownSites
- Remade VEP install assembly flag to be array and used rerun install for each assembly version
- Remade SnpEff install genomeVersion flag to be array and used rerun download for each genome version
- Added assembly flag to VEP script and alias it to use GRCh prefix and number
- Fixed chr prefix for chanjo sex check
- Updated to GATK version 3.6
- Created contig splitted target files on the fly for non genome analysis to reduce the running time of GATK Realign, BaseRecal and Haplotype
- Added sub ReplaceIUPAC and used it on freebayes and samtools mpileup vcfs
- Changed analysisType default from exomes to genomes

MIP v2.4 --> v2.6

- Updated GATK to 3.5
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5 changes: 3 additions & 2 deletions docs/installation.rst
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Expand Up @@ -28,7 +28,7 @@ installation.

.. code-block:: console
$ . mip.sh
$ bash mip.sh
This will install all the dependencies of MIP and other modules included in MIP into a conda environment (defaults to "mip").
However a fresh version of perl and cpanm is installed outside of the conda environment, but are activated through bashrc and bash_profile.
Expand All @@ -41,13 +41,14 @@ installation.
'export PATH=$HOME/perl-PERLVERSION/:$PATH' >> ~/.bashrc
'eval `perl -I ~/perl-PERLVERSION/lib/perl5/ -Mlocal::lib=~/perl-PERLVERSION/`' >> ~/.bash_profile
'export PERL_UNICODE=SAD' >> ~/.bash_profile
3. Run MIP

.. code-block:: console
$ source activate mip
$ perl mip.pl -h
$ mip.pl -h
Manual Installation
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25 changes: 14 additions & 11 deletions docs/setup.rst
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Expand Up @@ -17,35 +17,37 @@ Dependencies
Make sure you have loaded/installed all dependencies and that they are in your ``$PATH``.
You only need to load the dependencies that are required for the modules that you want to
run. If you fail to install dependencies for a module, MIP will tell you what dependencies
you need to install (or add to your ``$PATH``) and exit. Version after the software name
are tested for compatibility with MIP.
you need to install (or add to your ``$PATH``) and exit. MIP comes with an install script ``install.pl``,
which will install all necessary programs to execute models in MIP via bioconda and/or $SHELL.
Version after the software name are tested for compatibility with MIP.

**Program/Modules**

- Perl modules: YAML.pm, Log4perl.pm, List::MoreUtils, DateTime, DateTime::Format::ISO8601,
DateTime::Format::HTTP, DateTime::Format::Mail, Set::IntervalTree from CPAN, since these
are not included in the perl standard distribution
- Simple Linux Utility for Resource Management (`SLURM`_)
- `FastQC`_ (version: 0.11.4)
- `FastQC`_ (version: 0.11.5)
- `Mosaik`_ (version: 2.2.24)
- `BWA`_ (version: 0.7.12)
- `Sambamba`_ (version: 0.5.9)
- `BWA`_ (version: 0.7.13)
- `Sambamba`_ (version: 0.6.1)
- `SAMTools`_ (version: 1.3)
- `BedTools`_ (version: 2.25.0)
- `PicardTools`_ (version: 2.0.1)
- `Chanjo`_ (version: 3.3.0)
- `PicardTools`_ (version: 2.3.0)
- `Chanjo`_ (version: 3.4.1)
- `Manta`_ (version: 0.29.6)
- `GATK`_ (version: 3.5-0)
- `freebayes`_ (version: 1.2)
- `freebayes`_ (version: 1.0.2)
- `VT`_ (version: 0.5)
- `VEP`_ (version: 83) with plugin "UpDownDistance"
- `VEP`_ (version: 84) with plugin "UpDownDistance, LoFtool, LoF"
- vcfParser.pl (Supplied with MIP; see :doc:`vcfParser`)
- `SnpEff`_ (4.2)
- `ANNOVAR`_ (version: 2013-08-23)
- `GENMOD`_ (version: 3.4.8)
- `GENMOD`_ (version: 3.5.2)
- `VcfTools`_ (version: 0.1.14)
- `BcfTools`_ (version: 1.3)
- `PLINK`_ (version: 1.90b3x)
- `MultiQC`_ (version: 0.5)
- `MultiQC`_ (version: 0.6)

Depending on what programs you include in the MIP analysis you also need to add
these programs to your ``$PATH``:
Expand Down Expand Up @@ -136,6 +138,7 @@ directory using Annovars built-in download function.
.. _Chanjo: https://chanjo.readthedocs.org/en/latest/
.. _GATK: http://www.broadinstitute.org/gatk/
.. _freebayes: https://github.com/ekg/freebayes
.. _Manta: https://github.com/Illumina/manta
.. _VT: https://github.com/atks/vt
.. _VEP: http://www.ensembl.org/info/docs/tools/vep/index.html
.. _SnpEff: http://snpeff.sourceforge.net/
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