This repository is used to store scripts written during the hackathon of ALLBio Testcase 2. The aims of this project are:
- to provide a pipeline for Structural variation calling
- use this pipeline for benchmarking sv callers
More information about the project can be found at the following websites:
ALLBio Bioinformatics, Testcase#2, Google site, members only!
Grab a copy of this repository from GitHub to your home folder and store this in allbiotc2:
cd ~
git clone https://github.com/ALLBio/allbiotc2.git
cd allbiotc2/
make install
The make install command will do a system-wide install. This step requires sudo rights.
If reference calls are provided in SDI format, the following procedure can be followed to convert from SDI to VCF.
make -f ../scripts/Makefile \
REFERENCE_VCF=~/myworkdir/ref_all.complete.vcf \
SDI_FILE=~/myworkdir/ler_0.v7c.sdi \
preprocess
The software for the pipeline is placed into one central location in the following setup:
allbio@workbench:/virdir/Scratch/software$ tree -L 1
.
├── bowtie2-2.1.0
├── breakdancer
├── bwa-0.7.4
├── circos-0.63-4
├── clever-sv
├── delly_v0.0.9
├── dwac-seq0.7
├── FastQC
├── gasv
├── picard-tools-1.86
├── pindel
├── PRISM_1_1_6
├── samtools-0.1.19
├── sickle-master
└── SVDetect_r0.8b
Configuration can be done in the conf.mk and upon invocation of the pipeline by passing them via the commandline.
The most important and required variables are:
PROGRAMS: Path to the directory where the programs are installedPYTHON_EXE: Path to thePYTHONexecutable, defaults topython(system distributed version)REFERENCE_DIR: Path to the referenceREFERENCE_VCF: Full path to the VCF file with reference SV calls for benchmarkingFASTQ_EXTENSION: Filename extentension of the FastQ filesPEA_MARK: Filenaming of the left read of FastQ: sample-PEA_MARK.FASTQ_EXTENSIONPEB_MARK: Filenaming of the right read of FastQ: sample-PEB_MARK.FASTQ_EXTENSION*_THREADS: Set the amount of cores to used by the programs.
Example invocation of the pipeline:
THREADS=8
make -f ../scripts/Makefile \
PROGRAMS=/virdir/Scratch/software\
REFERENCE_DIR=../input/reference_tair9 \
FASTQC_THREADS=$THREADS \
BWA_OPTION_THREADS=$THREADS \
PEA_MARK=.1 \
PEB_MARK=.2 \
FASTQ_EXTENSION=fastq \
REFERENCE_VCF=/virdir/Backup/reads_and_reference/vcf_reference/ref_all.complete.vcf
allbio@workbench:/opt/allbio/runs/synthetic_run$ tree -L 1
.
├── input
│ ├── reference_tair10
│ │ ├── bowtie2
│ │ ├── bwa
│ │ ├── reference.fa
│ │ └── reference.fa.fai
│ ├── sim-reads_1.fastq
│ ├── sim-reads_2.fastq
│ ├── sim-reads.409_10.1.fastq
│ ├── sim-reads.409_10.2.fastq
│ ├── sim-reads.511_10.1.fastq
│ ├── sim-reads.511_10.2.fastq
├── log
├── run_integrationtest
│ ├── bd.cfg
│ ├── comparison.tex
│ ├── run.sh
│ ├── sim-read-511_10.1.fastq -> ../input/sim-reads.511_10.1.fastq
│ ├── sim-read-511_10.1.filtersync.stats
│ ├── sim-read-511_10.1.singles.fastq
│ ├── sim-read-511_10.1.trimmed.fastq
│ ├── sim-read-511_10.2.fastq -> ../input/sim-reads.511_10.2.fastq
│ ├── sim-read-511_10.2.trimmed.fastq
│ ├── sim-read-511_10.bam
│ ├── sim-read-511_10.bam.bai
│ ├── sim-read-511_10.bd.vcf
│ ├── sim-read-511_10.breakdancer
│ ├── sim-read-511_10.delly
│ ├── sim-read-511_10.delly.vcf
│ ├── sim-read-511_10.flagstat
│ ├── sim-read-511_10.gasv
│ ├── sim-read-511_10.gasv.vcf
│ ├── sim-read-511_10.pindel
│ ├── sim-read-511_10.pindel.vcf
│ ├── sim-read-511_10.prism
│ ├── sim-read-511_10.prism.vcf
│ ├── sim-read-511_10.raw_fastqc
│ ├── sim-read-511_10.sam
│ ├── sim-read-511_10.trimmed_fastqc
│ └── sim-read-511_10.unsort.bam
└── scripts
└── Makefile -> ~/allbiotc2/Makefile
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