HapKled: a haplotype-aware structural variant calling approach for Oxford Nanopore sequencing data

Usage

Before running HapKled you should first compile (see compiling the haplotype-aware kled) the haplotype-aware kled and put the path of it to the environment variable HapAwareKled.

export HapAwareKled=/path/to/hap-aware-kled

And you also need an installed Clair3 and Whatshap, and export the path of the Clair3 models to environment variable Clair3ModelPath.

export Clair3ModelPath=/path/to/bin/models

HapKled need a reference file (fasta) and at least one bam (sam/bam/cram) file that stores the mapped reads to call SVs, and output a VCF file to the standard output.

HapKled -R Refernce.fa Sample.bam > SVs.vcf

For the description of all parameters:

HapKled --help

Compiling the haplotype-aware kled

Dependencies: openmp and dependencies of htslib (-lz -lm -lbz2 -llzma -lcurl -lpthread -lcrypto -ldeflate)

Here are instructions to get some dependencies from source if systemwide installation is not available:

• zlib: download from https://github.com/madler/zlib/releases, unzip and cd and ./configure && make && make install prefix=/path/to/your/local
• libbz2: download from https://sourceforge.net/projects/bzip2/, unzip and cd and make && make install PREFIX=/path/to/your/local And export CPATH to make compiler know where the lib is: export CPATH=/path/to/your/local/include:$CPATH

You also need a compiler that supports C++ 17 standard.

To get the kled binary:

#to get htslib
git submodule update --init --recursive

#make kled
make

If you want to install kled:

make install
#or if you want to install to a place other than /usr/local:
PREFIX=PATH_YOU_SELECT make install

Experiments

You should run the run.sh in the experiments/simulation/run.sh to get the simulated bam, and along with it, put the downloaded bams and fastas to the $DataDir.

Then run experiments/benchmark/run.sh to get the benchmark results.