Commit cb301c65 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 5.0.3+git20151221.80e144e+dfsg

parent 11bf1b06

README.md

0 → 100644
+165 −0
Original line number Diff line number Diff line 
# Ion Torrent Variant Caller



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.



### Quick Start

```

git clone https://github.com/domibel/IonTorrent-VariantCaller.git



BASE=`pwd`

TVC_SOURCE_DIR=$BASE/IonTorrent-VariantCaller



*** adjust build and install directory ***

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 $TVC_SOURCE_DIR -DCMAKE_INSTALL_PREFIX:PATH=$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

```





### Get reference genome hg19 from Ion Torrent, Size: 868170684 (828M)



##### Download zip archive

```

$ wget http://ionupdates.com/reference/hg19.zip

```



##### Unpack zip archive

```

$ unzip hg19.zip

```



##### Create hg19.fasta.fai

```

$ samtools faidx hg19.fasta    

```



##### Content

```

$ md5sum hg19.zip hg19.fasta hg19.fasta.fai

21afdf14b6b3734e0d25157e60bdfb24  hg19.zip

d6851f9f4537ff4e9beb5b7a08b89230  hg19.fasta

cdcd61262b6f4af8e8ac6c2be88a161a  hg19.fasta.fai



$ ls -l

-rw-r--r-- 1 ionadmin ionadmin 3147289017 Mar 22  2011 hg19.fasta

-rw-rw-r-- 1 ionadmin ionadmin        788 Nov 18 16:18 hg19.fasta.fai

-rw-rw-r-- 1 ionadmin ionadmin  868170684 Jul  8  2014 hg19.zip

```



### Examples



#### 316 - H. sapiens - AmpliSeq BRCA1/BRCA2 Community Panel

##### https://ioncommunity.thermofisher.com/docs/DOC-7515

##### CN:TorrentServer/BRCA   PL:IONTORRENT   PU:PGM/316D/IonXpress_009

```

wget http://ion-torrent.s3.amazonaws.com/pgm/BRCArun94/BRCArun94IonXpress_009_rawlib.bam          # 163535738 156M

wget http://ion-torrent.s3.amazonaws.com/pgm/BRCArun94/BRCArun94IonXpress_009_rawlib.bam.bai      #   1675968 1.6M

wget http://ion-torrent.s3.amazonaws.com/pgm/BRCArun94/BRCArun94TSVC_variants_IonXpress_009.vcf   #     85850 84K



variant_caller_pipeline.py \

 --input-bam BRCArun94IonXpress_009_rawlib.bam \

 --reference-fasta hg19.fasta \

 --parameters-file=/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json \

 --generate-gvcf=on \

 --num-threads=4

```





#### Alternative: Get reference genome hg19 with TMAP index files from Ion Torrent, Size: 4613331358 (4.3G)



```

$ wget http://ionupdates.com/reference_downloads/hg19.zip

$ unzip hg19.zip

```



##### Content

```

$ md5sum *

d2dacce998d72687ca1f2dd28ce2280e  CreateSequenceDictionary.log

d264f416c20f7d144d74924ab7c356a0  hg19.dict

d6851f9f4537ff4e9beb5b7a08b89230  hg19.fasta

cdcd61262b6f4af8e8ac6c2be88a161a  hg19.fasta.fai

6903f05eef92e5e6f5a6bf890a01d6e6  hg19.fasta.tmap.anno

f9d7c7dedf322022a0393d99a629229b  hg19.fasta.tmap.bwt

19c79b65021812df67904f7448367d5f  hg19.fasta.tmap.pac

ebd201bec6945900ce9f26b62cf89915  hg19.fasta.tmap.sa

09b3113801b9c6ae69134f8712ef6a8c  hg19.info.txt

3bc8b68ce604c77f2fecd14ab20a13bc  hg19.md5sum.txt

3b725f35b395cf763bb7ac2110ab8d1a  hg19.zip

d41d8cd98f00b204e9800998ecf8427e  samtools.log

b9ba9df7fc3cd18883e7922bc6dd20d6  tmap.log

```

```

$ ls -l

total 13218824

-rwxr-xr-x 1 ionadmin ionadmin        624 May  6  2013 CreateSequenceDictionary.log

-rwxr-xr-x 1 ionadmin ionadmin       3174 May  6  2013 hg19.dict

-rwxr-xr-x 1 ionadmin ionadmin 3147289017 May  6  2013 hg19.fasta

-rwxr-xr-x 1 ionadmin ionadmin        788 May  6  2013 hg19.fasta.fai

-rwxr-xr-x 1 ionadmin ionadmin       3985 May  6  2013 hg19.fasta.tmap.anno

-rwxr-xr-x 1 ionadmin ionadmin 3453608024 May  6  2013 hg19.fasta.tmap.bwt

-rwxr-xr-x 1 ionadmin ionadmin  773923497 May  6  2013 hg19.fasta.tmap.pac

-rwxr-xr-x 1 ionadmin ionadmin 1547847008 May  6  2013 hg19.fasta.tmap.sa

-rwxr-xr-x 1 ionadmin ionadmin         92 May  6  2013 hg19.info.txt

-rwxr-xr-x 1 ionadmin ionadmin        642 May  6  2013 hg19.md5sum.txt

-rw-rw-r-- 1 ionadmin ionadmin 4613331358 Jul  8  2014 hg19.zip

-rwxr-xr-x 1 ionadmin ionadmin          0 May  6  2013 samtools.log

-rwxr-xr-x 1 ionadmin ionadmin      15170 May  6  2013 tmap.log

```





See also https://ioncommunity.thermofisher.com/community/products/software/torrent-variant-caller

README.txt

0 → 100644
+198 −0
Original line number Diff line number Diff line 
Compilation instructions for TVC



# Steps 1 through 11 explain how to compile TVC.

# Step 12 onward explain how to deploy and run the compiled version on a single computer or cluster.



For more information see:

http://ioncommunity.lifetechnologies.com/community/products/torrent-variant-caller



# 1. Download source file



wget updates.iontorrent.com/tvc_standalone/tvc-5.0.3.tar.gz





# 2. Copy source file into build root directory



TVC_VERSION=tvc-5.0.3



BUILD_ROOT_DIR=`mktemp -d`

cp $TVC_VERSION.tar.gz $BUILD_ROOT_DIR

DISTRIBUTION_CODENAME=`lsb_release -is`_`lsb_release -rs`_`uname -m`

TVC_INSTALL_DIR=$BUILD_ROOT_DIR/$TVC_VERSION-$DISTRIBUTION_CODENAME-binary

mkdir -p $TVC_INSTALL_DIR/bin/



# 3. Install dependencies



# 3.1 RedHat/CentOS



yum -y install gcc-c++ cmake zlib-devel bzip2-devel bzip2 \

ncurses-devel python-simplejson atlas-devel blas-devel lapack-devel redhat-lsb-core boost-devel \

# perl perl-Data-Dumper # with version 7





# 3.2 Debian/Ubuntu



sudo aptitude install g++ cmake zlib1g-dev libbz2-dev libncurses-dev libboost-math-dev \

libatlas-dev liblapack-dev





# 3.3 cmake



# Required is cmake (>=2.8.0), you can check the installed version with e.g.:



#  $ cmake -version

#  cmake version 2.8.0



# Installation of a newer cmake version is only required if the installed version is older than 2.8.0



# To delete the old cmake package:



# Redhat/CentOS:

yum -y erase cmake



# Debian/Ubuntu:

aptitude purge cmake



cd ~

wget http://www.cmake.org/files/v2.8/cmake-2.8.11.2.tar.gz

tar xvzf cmake-2.8.11.2.tar.gz

cd cmake-2.8.11.2

./configure

make -j5

make install





# 4. build armadillo

cd $BUILD_ROOT_DIR

wget http://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





# 5. build bamtools

cd $BUILD_ROOT_DIR

wget 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





# 7. build htslib

cd $BUILD_ROOT_DIR

wget --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





# 8. build samtools

cd $BUILD_ROOT_DIR

wget --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

cp samtools $TVC_INSTALL_DIR/bin/





# 10. build TVC

cd $BUILD_ROOT_DIR

tar xvzf $TVC_VERSION.tar.gz

TVC_SOURCE_DIR=$BUILD_ROOT_DIR/$TVC_VERSION

mkdir $TVC_VERSION-build

cd $TVC_VERSION-build

cmake $TVC_SOURCE_DIR -DCMAKE_INSTALL_PREFIX:PATH=$TVC_INSTALL_DIR -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo

make -j4 install



# 11. create binary package

tar cvzf $TVC_VERSION-$DISTRIBUTION_CODENAME-binary.tar.gz -C $BUILD_ROOT_DIR $TVC_VERSION-$DISTRIBUTION_CODENAME-binary





######################################################################################



# 12.1 Either use the TVC version from the (temporary) TVC_INSTALL_DIR directory



TVC_ROOT_DIR=$TVC_INSTALL_DIR





# 12.2 or use the TVC binary package



tar xvzf $TVC_VERSION-$DISTRIBUTION_CODENAME-binary.tar.gz

TVC_ROOT_DIR=`pwd`/$TVC_VERSION-$DISTRIBUTION_CODENAME-binary





# 13. export PATH, following tools are required: samtools zip tvc

export PATH=$PATH:$TVC_ROOT_DIR/bin





# 14. adjust some file paths and invoke TVC



# Required are 1 reference, 2 bed files, 1 aligned bam file, and 1 tvc parameter file



# Example 1:



$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



# Example 1 with specified parameter file and output directory:



$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 \

    --parameters-file $TVC_ROOT_DIR/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json \

    --output-dir      /tmp/tvc_example1





# Example 2 (not included yet) :



# Required are 1 reference, 2 bed files, 1 aligned bam file, and 1 tvc parameter file

                REF=/mnt/TS/source/hg19/hg19.fasta

BED_UNMERGED_DETAIL=/mnt/TS/source/tvc_test_GB1-118-CSI/unmerged/detail/Exome_draft_Designed_20130531.bed

   BED_MERGED_PLAIN=/mnt/TS/source/tvc_test_GB1-118-CSI/merged/plain/Exome_draft_Designed_20130531.bed

                BAM=/mnt/TS/source/tvc_test_GB1-118-CSI/IonXpress_045_rawlib.bam

          TVC_PARAM=$TVC_ROOT_DIR/share/TVC/pluginMedia/configs/germline_low_stringency_proton.json



TMP_DIR=`mktemp -d`



$TVC_ROOT_DIR/bin/variant_caller_pipeline.py \

    --parameters-file $TVC_PARAM \

    --input-bam $BAM \

    --reference-fasta $REF \

    --region-bed $BED_MERGED_PLAIN \

    --primer-trim-bed $BED_UNMERGED_DETAIL \

    --postprocessed-bam $TMP_DIR/trimmed.bam \

    --output-dir $TMP_DIR





# Example 3 (hotspot) (not included yet):



                REF=/mnt/TS/source/hg19/hg19.fasta

BED_UNMERGED_DETAIL=/mnt/TS/source/tvc_test_Z06-506-CCP/unmerged_detail_CCP.20131001.designed.bed

   BED_MERGED_PLAIN=/mnt/TS/source/tvc_test_Z06-506-CCP/merged_plain_CCP.20131001.designed.bed

                BAM=/mnt/TS/source/tvc_test_Z06-506-CCP/IonXpress_019_rawlib.bam

          TVC_PARAM=/mnt/TS/source/tvc_test_Z06-506-CCP/local_parameters.json

            HOTSPOT=/mnt/TS/source/tvc_test_Z06-506-CCP/hotspot.vcf



TMP_DIR=`mktemp -d`



time $TVC_ROOT_DIR/bin/variant_caller_pipeline.py \

    --parameters-file $TVC_PARAM \

    --input-bam $BAM \

    --reference-fasta $REF \

    --region-bed $BED_MERGED_PLAIN \

    --primer-trim-bed $BED_UNMERGED_DETAIL \

    --hotspot-vcf $HOTSPOT \

    --postprocessed-bam $TMP_DIR/trimmed.bam \

    --output-dir $TMP_DIR

external/vcflib/smithwaterman/BandedSmithWaterman.cpp

deleted100644 → 0
+0 −670

File deleted.

Preview size limit exceeded, changes collapsed.

external/vcflib/smithwaterman/BandedSmithWaterman.h

deleted100644 → 0
+0 −111
Original line number Diff line number Diff line 
#pragma once



#include <iostream>

#include <algorithm>

#include <memory>

//#include "Alignment.h"

#include "Mosaik.h"

//#include "HashRegion.h"

#include <string.h>

#include <stdio.h>

#include <sstream>

#include <string>



using namespace std;



#define MOSAIK_NUM_NUCLEOTIDES 26

#define GAP '-'



typedef unsigned char DirectionType;

typedef unsigned char PositionType;



struct ElementInfo {

	unsigned int Direction             : 2;

	unsigned int mSizeOfVerticalGaps   : 15;

	unsigned int mSizeOfHorizontalGaps : 15;

};



class CBandedSmithWaterman {

public:

	// constructor

	CBandedSmithWaterman(float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty, unsigned int bandWidth);

	// destructor

	~CBandedSmithWaterman(void);

	// aligns the query sequence to the anchor using the Smith Waterman Gotoh algorithm

	void Align(unsigned int& referenceAl, string& stringAl, const string& s1, const string& s2, pair< pair<unsigned int, unsigned int>, pair<unsigned int, unsigned int> >& hr);

	// enables homo-polymer scoring

	void EnableHomoPolymerGapPenalty(float hpGapOpenPenalty);

private:

	// calculates the score during the forward algorithm

	float CalculateScore(const string& s1, const string& s2, const unsigned int rowNum, const unsigned int columnNum, float& currentQueryGapScore, const unsigned int rowOffset, const unsigned int columnOffset);

	// creates a simple scoring matrix to align the nucleotides and the ambiguity code N

	void CreateScoringMatrix(void);

	// corrects the homopolymer gap order for forward alignments

	void CorrectHomopolymerGapOrder(const unsigned int numBases, const unsigned int numMismatches);

	// returns the maximum floating point number

	static inline float MaxFloats(const float& a, const float& b, const float& c);

	// reinitializes the matrices

	void ReinitializeMatrices(const PositionType& positionType, const unsigned int& s1Length, const unsigned int& s2Length, const pair< pair<unsigned int, unsigned int>, pair<unsigned int, unsigned int> > hr);

	// performs the backtrace algorithm

	void Traceback(unsigned int& referenceAl, string& stringAl, const string& s1, const string& s2, unsigned int bestRow, unsigned int bestColumn, const unsigned int rowOffset, const unsigned int columnOffset);

	// updates the best score during the forward algorithm

	inline void UpdateBestScore(unsigned int& bestRow, unsigned int& bestColumn, float& bestScore, const unsigned int rowNum, const unsigned int columnNum, const float score);

	// our simple scoring matrix

	float mScoringMatrix[MOSAIK_NUM_NUCLEOTIDES][MOSAIK_NUM_NUCLEOTIDES];

	// keep track of maximum initialized sizes

	unsigned int mCurrentMatrixSize;

	unsigned int mCurrentAnchorSize;

	unsigned int mCurrentAQSumSize;

	unsigned int mBandwidth;

	// define our backtrace directions

	const static DirectionType Directions_STOP;

	const static DirectionType Directions_LEFT;

	const static DirectionType Directions_DIAGONAL;

	const static DirectionType Directions_UP;

	// store the backtrace pointers

	ElementInfo* mPointers;

	// define our position types

	const static PositionType Position_REF_AND_QUERY_ZERO;

	const static PositionType Position_REF_ZERO;

	const static PositionType Position_QUERY_ZERO;

	const static PositionType Position_REF_AND_QUERO_NONZERO;

	// define scoring constants

	const float mMatchScore;

	const float mMismatchScore;

	const float mGapOpenPenalty;

	const float mGapExtendPenalty;

	// score if xi aligns to a gap after yi

	float* mAnchorGapScores;

	// best score of alignment x1...xi to y1...yi

	float* mBestScores;

	// our reversed alignment

	char* mReversedAnchor;

	char* mReversedQuery;

	// define static constants

	static const float FLOAT_NEGATIVE_INFINITY;

	// toggles the use of the homo-polymer gap open penalty

	bool mUseHomoPolymerGapOpenPenalty;

	float mHomoPolymerGapOpenPenalty;

};



// returns the maximum floating point number

inline float CBandedSmithWaterman::MaxFloats(const float& a, const float& b, const float& c) {

	float max = 0.0f;

	if(a > max) max = a;

	if(b > max) max = b;

	if(c > max) max = c;

	return max;

}



// updates the best score during the forward algorithm

inline void CBandedSmithWaterman::UpdateBestScore(unsigned int& bestRow, unsigned int& bestColumn, float& bestScore, const unsigned int rowNum, const unsigned int columnNum, const float score) {



	//const unsigned int row    = rowNum + rowOffset;

	//const unsigned int column = columnOffset - rowNum + columnNum;



	if(score > bestScore) {

		bestRow    = rowNum;

		bestColumn = columnNum;

		bestScore  = score;

	}

}

external/vcflib/smithwaterman/IndelAllele.cpp

deleted100644 → 0
+0 −62
Original line number Diff line number Diff line 
#include "IndelAllele.h"



using namespace std;





bool IndelAllele::homopolymer(void) {

    string::iterator s = sequence.begin();

    char c = *s++;

    while (s != sequence.end()) {

        if (c != *s++) return false;

    }

    return true;

}



int IndelAllele::readLength(void) {

    if (insertion) {

	return length;

    } else {

	return 0;

    }

}



int IndelAllele::referenceLength(void) {

    if (insertion) {

	return 0;

    } else {

	return length;

    }

}



bool homopolymer(string sequence) {

    string::iterator s = sequence.begin();

    char c = *s++;

    while (s != sequence.end()) {

        if (c != *s++) return false;

    }

    return true;

}



ostream& operator<<(ostream& out, const IndelAllele& indel) {

    string t = indel.insertion ? "i" : "d";

    out << t <<  ":" << indel.position << ":" << indel.readPosition << ":" << indel.length << ":" << indel.sequence;

    return out;

}



bool operator==(const IndelAllele& a, const IndelAllele& b) {

    return (a.insertion == b.insertion

            && a.length == b.length

            && a.position == b.position

            && a.sequence == b.sequence);

}



bool operator!=(const IndelAllele& a, const IndelAllele& b) {

    return !(a==b);

}



bool operator<(const IndelAllele& a, const IndelAllele& b) {

    ostringstream as, bs;

    as << a;

    bs << b;

    return as.str() < bs.str();

}