Created
March 18, 2019 09:50
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run Nirvana
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| # ubuntu 18.04 | |
| wget -q https://packages.microsoft.com/config/ubuntu/18.04/packages-microsoft-prod.deb | |
| sudo dpkg -i packages-microsoft-prod.deb | |
| sudo add-apt-repository universe | |
| sudo apt-get install -y apt-transport-https | |
| sudo apt-get update | |
| sudo apt-get install -y dotnet-sdk-2.2 | |
| mkdir Nirvana | |
| cd Nirvana | |
| wget https://github.com/Illumina/Nirvana/releases/download/v2.0.3/2.0.3.zip | |
| unzip 2.0.3.zip | |
| wget https://illumina-annotation.s3.amazonaws.com/Cache/v24.tar.gz | |
| wget https://illumina-annotation.s3.amazonaws.com/References/v5.tar.gz | |
| wget https://illumina-annotation.s3.amazonaws.com/SA/41/v41_GRCh37.tar.gz | |
| wget https://illumina-annotation.s3.amazonaws.com/SA/41/v41_GRCh38.tar.gz | |
| tar axvf v24.tar.gz | |
| tar axvf v41_GRCh37.tar.gz | |
| tar axvf v41_GRCh38.tar.gz | |
| tar axvf v5.tar.gz | |
| md SupplementaryDatabase/41 | |
| mv GRCh37 SupplementaryDatabase/41 | |
| mv GRCh38 SupplementaryDatabase/41 | |
| dotnet Nirvana.dll -c Cache/24/GRCh37/Both84 --sd SupplementaryDatabase/41/GRCh37 -r References/5/Homo_sapiens.GRCh37.Nirvana.dat -i sample.vcf -o sample | |
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