生信软件46 - 三代测序低深度全基因组测序结构变异SV检测工具NanoVar-CSDN博客

本文链接：https://blog.csdn.net/LittleComputerRobot/article/details/147741372

1. NanoVar简介

NanoVar 是一种新颖的 SV 识别工具，在准确性和速度方面表现出色，同时克服了三代测序全基因组测序（WGS）低深度和易出错的问题 。在模拟数据中， NanoVar 在仅使用 4 - 8X 覆盖度的数据集检测纯合和杂合 SV ，优于现有的三代测序结构变异（SV）检测工具，实现了较高的 SV 检测准确率（F1>0.92）。NanoVar 的性能在低深度真实数据（如样本 NA12878）和临床数据中也得到了体现，并可靠地推断 SV 的类别、大小和杂合性。模拟和真实数据的结果都表明，4X 测序深度可能不足以全面发现杂合 SV，建议使用 8X 或更高测序深度。

参考文献：
Tham, CY., Tirado-Magallanes, R., Goh, Y. et al. NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing. Genome Biol. 21, 56 (2020). https://doi.org/10.1186/s13059-020-01968-7

使用NA12878标准品，在4X深度下，不同的三代SVs检测工具，检测缺失SVs时SVIM召回率最高（0.78）、nanoVar (0.71)、 Sniffles (0.58),and Picky(0.54)；对于插入SVs，nanovar召回率最高（0.66)）、SVIM (0.62),、Sniffles (0.28) and Picky (0.22)。在8X深度下，nanova和SVIM召回率接近0.82。

github地址： https://github.com/benoukraflab/NanoVar

不同测序深度(4X 8X 12X)纯合/杂合SVs检测准确率和召回率:
不同测序深度纯合/杂合SVs检测准确率和召回率
2代测序和3代测序SVs检测工具比较：

输出结果：

2. 安装依赖

软件版本要求：

bedtools >=2.26.0
samtools >=1.3.0
minimap2 >=2.17

conda create -n nanovar -c bioconda python=3.9
conda activate nanovar

conda insatall bedtools -y
conda install samtools==1.3.0 -y
conda install minimap2==2.17 -y
conda install seqtk -y

# 安装nanovar
conda install nanovar==1.8.0 -y

3. 基本用法

# -t: 线程数
# -x: 三代测序数据类型，支持ont, pacbio-clr, pacbio-ccs
# -f: 参考基因组gap bed文件或调用内置hg19、hg38和mm10 gap bed
# sample.bam: 样本碧迪排序后BAM文件
# ref.fa： 参考基因组fasta文件
# working_dir： 工作目录

# ONT数据
nanovar -t 10 -x ont -f hg38 sample.bam ref.fa working_dir

4. 参数说明

usage: nanovar [options] [FASTQ/FASTA/BAM/CRAM] [REFERENCE_GENOME] [WORK_DIRECTORY]

positional arguments:
  [FASTQ/FASTA/BAM/CRAM]
                        Path to long reads or mapped BAM/CRAM file.
                        Formats: fasta/fa/fa.gzip/fa.gz/fastq/fq/fq.gzip/fq.gz/bam/cram
  [reference_genome]    Path to reference genome in FASTA. Genome indexes created
                        will overwrite indexes created by other aligners such as bwa.
  [work_directory]      Path to work directory. Directory will be created
                        if it does not exist.

options:
  -h, --help            show this help message and exit
  -x str, --data_type str
                        Type of long-read data [ont]
                        ont - Oxford Nanopore Technologies
                        pacbio-clr - Pacific Biosciences CLR
                        pacbio-ccs - Pacific Biosciences CCS
  -f file, --filter_bed file
                        BED file with genomic regions to be excluded [None]
                        (e.g. telomeres and centromeres) Either specify name of in-built
                        reference genome filter (i.e. hg38, hg19, mm10) or provide full
                        path to own BED file.
  --annotate_ins str    Enable annotation of INS with NanoINSight,
                        please specify species of sample [None]
                        Currently supported species are:
                        'human', 'mouse', and 'rattus'.
  -c int, --mincov int  Minimum number of reads required to call a breakend [4]
  -l int, --minlen int  Minimum length of SV to be detected [25]
  -p float, --splitpct float
                        Minimum percentage of unmapped bases within a long read
                        to be considered as a split-read. 0.05<=p<=0.50 [0.05]
  -a int, --minalign int
                        Minimum alignment length for single alignment reads [200]
  -b int, --buffer int  Nucleotide length buffer for SV breakend clustering [50]
  -s float, --score float
                        Score threshold for defining PASS/FAIL SVs in VCF [1.0]
                        Default score 1.0 was estimated from simulated analysis.
  --homo float          Lower limit of a breakend read ratio to classify a homozygous state [0.75]
                        (i.e. Any breakend with homo<=ratio<=1.00 is classified as homozygous)
  --hetero float        Lower limit of a breakend read ratio to classify a heterozygous state [0.35]
                        (i.e. Any breakend with hetero<=ratio<homo is classified as heterozygous)
  --sv_bam_out          Outputs a BAM file containing only SV-supporting reads with
                        their corresponding SV-ID(s) stored in the "nv" tag separated by comma.
  --debug               Run in debug mode
  -v, --version         Show version and exit
  -q, --quiet           Hide verbose
  -t int, --threads int
                        Number of available threads for use [1]
  --model path          Specify path to custom-built model
  --mm path             Specify path to 'minimap2' executable
  --st path             Specify path to 'samtools' executable
  --ma path             Specify path to 'mafft' executable for NanoINSight
  --rm path             Specify path to 'RepeatMasker' executable for NanoINSight