ALLBio testcase #2

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!

How to install

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.

Preprocessing reference VCF (optional)

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

Installing the software

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

Running the pipeline

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 installed
• PYTHON_EXE: Path to the PYTHON executable, defaults to python (system distributed version)
• REFERENCE_DIR: Path to the reference
• REFERENCE_VCF: Full path to the VCF file with reference SV calls for benchmarking
• FASTQ_EXTENSION: Filename extentension of the FastQ files
• PEA_MARK: Filenaming of the left read of FastQ: sample-PEA_MARK.FASTQ_EXTENSION
• PEB_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 

Example setup of pipeline directories

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