Pynnotator New Release!

This new release brings a lot more stability for this annotation pipeline!

Now you can use Docker for running in any machine and also it accepts .vcf and .vcf.gz files as an input.

I updated all the tools (Ex. snpeff and vep) and databases (decipher, 1000genomes, dbsnp and dbnfsp)
Data and Lib Files are now hosted on Google Cloud!

Files
.
├── 1000genomes
│   ├── ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
│   └── ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi
├── dbnsfp
│   ├── dbNSFP3.4a.txt.gz
│   ├── dbNSFP3.4a.txt.gz.tbi
│   ├── dbscSNV1.1.txt.gz
│   └── dbscSNV1.1.txt.gz.tbi
├── dbsnp
│   ├── All_20170403.vcf.gz
│   ├── All_20170403.vcf.gz.tbi
│   ├── clinvar.vcf.gz
│   └── clinvar.vcf.gz.tbi
├── decipher
│   ├── DDG2P.csv.gz
│   ├── HI_Predictions_Version3.bed.gz
│   ├── HI_Predictions_Version3.bed.gz.tbi
│   └── population_cnv.txt.gz
├── ensembl
│   ├── Homo_sapiens_clinically_associated.vcf.gz
│   ├── Homo_sapiens_clinically_associated.vcf.gz.tbi
│   ├── Homo_sapiens_phenotype_associated.vcf.gz
│   └── Homo_sapiens_phenotype_associated.vcf.gz.tbi
├── esp6500
│   ├── esp6500si.vcf.gz
│   └── esp6500si.vcf.gz.tbi
├── snpeff_data
│   └── GRCh37.75
└── vep_cache
└── homo_sapiens
└── 88_GRCh37

705 directories, 11839 files

Examples
.
├── annotation.validated.vcf.gz
├── examples
│   ├── miller.vcf.gz
│   ├── NA12878.compound_heterozygous.vcf.gz
│   ├── NA12878.dominant.vcf.gz
│   ├── NA12878.recessive.vcf.gz
│   ├── NA12878.xlinked.vcf.gz
│   └── schinzel_giedion.vcf.gz
└── sample.1000.vcf


How to run it?
==============

Requires at least 65GB of disk space during installation and 35GB after installed.

1º Method::

docker-compose run pynnotator -i pynnotator/tests/sample.1000.vcf
or
docker-compose run pynnotator -i sample.vcf.gz

2º Method::

# Using Ubuntu 16.04 LTS

sudo apt-get install gcc git python3-dev zlib1g-dev virtualenvwrapper make zip
source /etc/bash_completion.d/virtualenvwrapper
mkvirtualenv -p /usr/bin/python3 mendelmd
pip install cython
pip install pynnotator
pynnotator install

#And them finally:
pynnotator -i sample.vcf
#or
pynnotator -i sample.vcf.gz

 https://github.com/raonyguimaraes/pynnotator

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