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