LRAPsv

LRAPsv is a germline structural variant caller for long-reads.

Installation

Step1 configure the conda source

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
conda config --set show_channel_urls yes

Step2 install LRAPsv

conda create -n LRAPsv python=3.9.5 -y
conda activate LRAPsv
pip install sniffles==2.0.7
conda install -c bioconda bcftools=1.17 tabix openssl=1.1.1w -y
git clone https://github.com/Roick-Leo/LRAPsv.git
chmod -R a+x ./LRAPsv

Usage

./LRAPsv.bin \
-r ${REFERENCE} \
-i ${INPUT_BAM} \
-t ${THREADS} \
-mq ${MAP QUANLITY} \
-v ${OUTPUT}

Demo

minimap2 -ax map-ont --secondary=no -t 15 /path/to/reference.fa /path/to/fastq_file | samtools view -@ 15 -bS | samtools sort -@ 15 -o /path/to/output_sorted.bam

conda activate LRAPsv
/path/to/LRAPsv.bin -r /path/to/reference.fa -i /path/to/Sample_sorted.bam -v /path/to/output.vcf -t 15

Final comparison

truvari -f ref/human_hs37d5.fasta -b giab/HG002_SVs_Tier1_v0.6.vcf.gz\
        --includebed giab/HG002_SVs_Tier1_v0.6.bed -o bench-pbsv --passonly\
        --giabreport -r 1000 -p 0.00 -c /path/to/hg2.vcf.gz

Contact

• He Lei
  • Email: [email protected]