Ion Torrent Variant Caller

Owned by Indy Siva
Last updated: Jun 20, 2016
1 min read

 

Introduction

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

module load bioinformatics/tvc

 

Installation

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`
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 $TVC_BUILD_DIR
mkdir TVC-build
cd TVC-build
#Copy boost stuff in src dir
cp -r  /sw/library/boost/1.60.0/ser/include/boost /sw/bioinformatics/IonTorrent-VariantCaller
cmake /sw/bioinformatics/IonTorrent-VariantCaller  -DCMAKE_INSTALL_PREFIX:PATH=$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
 
 

 

Reference

 

  1. https://github.com/domibel/IonTorrent-VariantCaller