Sniffles使用简介
介绍:
Sniffles用于检测长读长数据的SV。主要为Pacbio数据而设计,但对于Oxford Nanopore数据也是可以的。SV是基因组上的大片段事件(例如,deletion,duplication,insertion,inversion and translocation)。Sniffles能检测这些类型也能检测巢式SV(例如,inversion周围存在deletion或invert duplication)。
下载:
https://github.com/fritzsedlazeck/Sniffles/releases
安装:
wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz
tar xzvf Sniffles.tar.gz
cd Sniffles-master/
mkdir -p build/
cd build/
# 可下载编译好的cmake进行软件的编译
cmake ..
make
快速使用:
./sniffles -m mapped.sort.bam -v output.vcf
-m 排序后的BAM文件
-v 输出vcf文件
群call(population SV calling)
以下介绍如何使用Sniffles和SURVIVOR获取多样本VCF文件
(1)获取各个样本的VCF
首先使用sniffles对各个样本进行SV的鉴定:
sniffles -m my_sample.bam -v my_sample.vcf
(2)合并多个样本的VCF
首先,获取SURVIVOR软件,下载:https://github.com/fritzsedlazeck/SURVIVOR
使用说明:https://github.com/fritzsedlazeck/SURVIVOR/wiki
a. 合并文件前需要进行排序
b. 将所有VCF文件的路径放入一个文件,例如:
ls *sample.vcf > vcf_files_raw_calls.txt
c. 使用SURVIVOR将这些文件进行合并,生成一个VCF文件:
SURVIVOR merge vcf_files_raw_calls.txt 1000 1 1 -1 -1 -1merged_SURVIVOR_1kbpdist_typesave.vcf
该步骤生成了共有的SV事件,但是没有保留各个样本特有的SV信息。
(3)强制检测所有样本的SVs
基于全部样本再次运行sniffles,例如:
sniffles -m my_sample.bam -v my_sample_gt.vcf --Ivcfmerged_SURVIVOR_1kbpdist_typesave.vcf
当各个样本完成运行后,再次合并VCF文件,同样将上述VCF文件路径写入到一个文件,例如:
ls *sample_gt.vcf > vcf_files_gt_calls.txt
然后运行SURVIVOR:
SURVIVOR merge vcf_files_gt_calls.txt 1000 -1 1 -1 -1 -1 merged_gt_SURVIVOR_1kbpdist_typesave.vcf
(The -1 for the minimum SV caller is necessary to obtain all calls even if they might be 0/0 in all samples.)
参考文献:
[1] Accurate and fast detection of complex and nested structural variations using long read technologies. Biological Data Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 26 - 29.10.2016.
[2] NGMLR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis. Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK, 19.09.-2.09.2016.
[3] Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature communications, Vol. 8, 14061, 24.01.2017, p. 1-11. DOI:10.1038/NCOMMS14061.
[4] Accurate detection of complex structural variations using single-molecule sequencing. Nature Methodsvolume 15, pages461–468 (2018).