An SV caller from paired-end NGS data.

In order to compile the code, the following are required:

• A C and a C++ compiler are required. If the GCC suite is used, version 4.9.3 or above is required.
• CMake (2.8 or above)

Downloaded the latest release from https://github.com/Mesh89/SurVeyor/releases , uncompress it and enter the directory. The following commands should be sufficient

./build_htslib.sh
cmake -DCMAKE_BUILD_TYPE=Release . && make

If you are compiling on the same platform as where you will execute it, you can use -DNATIVE=ON to create faster executables

cmake -DCMAKE_BUILD_TYPE=Release -DNATIVE=ON . && make

Python 3 is necessary to run SurVIndel2. Libraries NumPy (http://www.numpy.org/), PySam (https://github.com/pysam-developers/pysam) and xgboost (https://xgboost.readthedocs.io/en/stable/) are also necessary.

Please also download trained-model.zip from the release you are using, and uncompress it in a location of your convenience.

SurVeyor needs a BAM/CRAM file, a (possibly empty) working directory and reference genome in FASTA format. For the genotype command, it will also require an input VCF.

The BAM/CRAM file must be coordinate-sorted and indexed. Furthermore, the MD, MC and the MQ tag must be present for all primary alignments, when applicable.

Recent versions of BWA MEM (0.7.17) will add the MC tag. The easiest (but probably not the fastest) way to add the MQ tag is to use Picard FixMateInformation (http://broadinstitute.github.io/picard/command-line-overview.html#FixMateInformation)

java -jar picard.jar FixMateInformation I=file.bam

The basic command to call structural variants

python surveyor.py call --threads N_THREADS BAM_FILE WORKDIR REFERENCE_FASTA --ml-model TRAINED_MODEL

TRAINED_MODEL should be the location of the uncompressed trained-model.zip

For other parameters, please see the help with

python surveyor.py call -h

The basic command to genotype a set of structural variants in VCF format (IN_VCF) is

python surveyor.py genotype --threads N_THREADS IN_VCF OUT_VCF BAM_FILE WORKDIR REFERENCE_FASTA TRAINED_MODEL

where OUT_VCF is the location of the output VCF containing the genotyped variants.

For other parameters, please see the help with

python surveyor.py genotype -h

Currently, there is no manuscript for SurVeyor.

If you use deletions or tandem duplications, please cite: Rajaby, R., Sung, WK. SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads. Nat Commun 15, 10473 (2024). https://doi.org/10.1038/s41467-024-53087-7

If you use insertions, please cite: Rajaby, R., Liu, DX., Au, C.H. et al. INSurVeyor: improving insertion calling from short read sequencing data. Nat Commun 14, 3243 (2023). https://doi.org/10.1038/s41467-023-38870-2