Materials for Structural Variant Calling Section

Introduction

Here are some materials used for Structural Variant Calling section in Bioinformatic Summer school in Viet Nam 2017. Included:

• codes for reading BAM files
• example BAM file
• the gold standard of SVs called by Tardis

Reading BAM file

Libraries

There are some libraries used for reading BAM file in:

• C (htslib and samtools)
• C++ (Bamtools)
• Python (pysam).

You should take a look the example codes in this repository, which cointaining the API for reading BAM files, to implement your SV calling tool.

Installation

required: zlib

git clone --recurse-submodules https://github.com/SummerSchoolVN/SV_Materials
cd SV_Materials

### Install Bamtools

mkdir ./lib/bamtools/build && cd ./lib/bamtools/build
cmake ../
make

### Install htslib

cd /path/to/SV_Materials/lib/htslib
make

### Install pysam

sudo pip intall pysam

Make test

Some examples codes were provided for reading BAM file: test.cc, test.c, and test.py

cd /path/to/SV_Materials && make

Testing

Before testing, just add bammtool and htslib library into your LD_LIBRARY_PATH:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/bamtools/lib:/path/to/htslib

Then you could test the example codes as below:

python test.py <path to BAM file>

./test_c <path to BAM file>

./test.cc </path to BAM file>

BAM files and SV calling code

BAM file and the tool for calling SV could be download at: https://www.dropbox.com/s/5g11wamij3titbv/SV_Pred.tar.gz?dl=0

Standard result

Standard result could be downloaded at: https://www.dropbox.com/s/apy5e2p8h15fs99/CHM1_Del_pacBio.hg19.chr22%20%281%29.bed?dl=0