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Ion Torrent Variant Caller (TVC) is a genetic variant caller for Ion Torrent sequencing platforms, and is specially optimized to exploit the underlying flow signal information in the statistical model to evaluate variants. Torrent Variant Caller is designed to call single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), insertions, deletions, and block substitutions.
Usage
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module load bioinformatics/tvc |
Installation
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module load cmake/3.5.0 module load boost/1.60.0 module load gcc/4.9.3 cd /sw/bioinformatics git clone https://github.com/domibel/IonTorrent-VariantCaller.git cd /sw/bioinformatics/IonTorrent-VariantCaller BASE=`pwd` #BASE=/sw/bioinformatics/IonTorrent-VariantCaller TVC_SOURCE_DIR=$BASE/IonTorrent-VariantCaller TVC_BUILD_DIR=$BASE/IonTorrent-VariantCaller-build TVC_INSTALL_DIR=$BASE/IonTorrent-VariantCaller-install/usr/local mkdir -p $TVC_BUILD_DIR mkdir -p $TVC_INSTALL_DIR cd $TVC_BUILD_DIR wget --no-clobber updates.iontorrent.com/updates/software/external/armadillo-4.600.1.tar.gz tar xvzf armadillo-4.600.1.tar.gz cd armadillo-4.600.1/ sed -i 's:^// #define ARMA_USE_LAPACK$:#define ARMA_USE_LAPACK:g' include/armadillo_bits/config.hpp sed -i 's:^// #define ARMA_USE_BLAS$:#define ARMA_USE_BLAS:g' include/armadillo_bits/config.hpp cmake . make -j4 cd $TVC_BUILD_DIR wget --no-clobber updates.iontorrent.com/updates/software/external/bamtools-2.4.0.20150702+git15eadb925f.tar.gz tar xvzf bamtools-2.4.0.20150702+git15eadb925f.tar.gz mkdir bamtools-2.4.0.20150702+git15eadb925f-build cd bamtools-2.4.0.20150702+git15eadb925f-build cmake ../bamtools-2.4.0.20150702+git15eadb925f -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo make -j4 cd $TVC_BUILD_DIR wget --no-clobber --no-check-certificate https://github.com/samtools/htslib/archive/1.2.1.tar.gz -O htslib-1.2.1.tar.gz tar xvzf htslib-1.2.1.tar.gz ln -s htslib-1.2.1 htslib # for samtools cd htslib-1.2.1 make -j4 cd $TVC_BUILD_DIR wget --no-clobber --no-check-certificate https://github.com/samtools/samtools/archive/1.2.tar.gz -O samtools-1.2.tar.gz tar xvzf samtools-1.2.tar.gz cd samtools-1.2 make -j4 mkdir $TVC_INSTALL_DIR/bin cp samtools $TVC_INSTALL_DIR/bin/ cd $TVC_BUILD_DIR mkdir TVC-build cd TVC-build #cmake #Copy boost stuff in src dir cp -r /sw/library/boost/1.60.0/ser/include/boost /sw/bioinformatics/IonTorrent-VariantCaller/git cmake -DCMAKE_INSTALL_PREFIX:PATH=$TVC_INSTALL_DIR -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo cmake $TVC_SOURCE_DIR/sw/bioinformatics/IonTorrent-VariantCaller -DCMAKE_INSTALL_PREFIX:PATH=$TVC_INSTALL_DIR -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo make -j4 install *** quick test *** TVC_ROOT_DIR=$TVC_INSTALL_DIR $TVC_ROOT_DIR/bin/variant_caller_pipeline.py \ --input-bam $TVC_ROOT_DIR/share/TVC/examples/example1/test.bam \ --reference-fasta $TVC_ROOT_DIR/share/TVC/examples/example1/reference.fasta \ --region-bed $TVC_ROOT_DIR/share/TVC/examples/example1/test_merged_plain.bed \ --primer-trim-bed $TVC_ROOT_DIR/share/TVC/examples/example1/test_unmerged_detail.bed *** export PATH, following tools are required: samtools zip tvc *** export PATH=$PATH:$TVC_ROOT_DIR/bin |
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