2023-07-20 samtools软件的安装与使用

下载与安装

# Installing samtools (https://github.com/samtools/samtools/releases)
#wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 -P ~/software/
tar jxf ~/software/samtools-1.17.tar.bz2
cd samtools-1.17/
./configure --prefix=/opt/biosoft/samtools-1.17 && make -j 4 && make install
cd ../ && rm -rf samtools-1.17/
echo 'PATH=$PATH:/opt/biosoft/samtools-1.17/bin/' >> ~/.bashrc
source ~/.bashrc
#wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2 -P ~/software
tar jxf ~/software/samtools-0.1.19.tar.bz2 -C /opt/biosoft
cd /opt/biosoft/samtools-0.1.19/
make -j 4

练习

# Samtools Practise
cd /home/train/06.reads_aligment/bowtie2
samtools sort -@ 8 -o V1.bam -O BAM V1.sam #@表示cpu
samtools sort -@ 8 -o V2.bam -O BAM V2.sam
samtools index V1.bam #生成索引文件
samtools view -h V1.bam MS01Contig01:10000-20000 | less -S #查看目标区域的结果
samtools view -h -b V1.bam MS01Contig01 > V1.MS01Contig01.bam #-h可以得到头部
samtools view -h -f 64 V1.bam | samtools view -h -F 4 | les #-f表示结果filt和flag 64表示来自于reads1；-F 4表示该序列没有比对到参考序列上
samtools faidx genome.fasta MS01Contig02:40000-42000 | les #对fasta文件建立索引
/opt/biosoft/samtools-0.1.19/samtools tview V1.bam genome.fasta #

samtools view -b -f 64 V1.bam > V1.f64.bam
samtools index V1.f64.bam
/opt/biosoft/samtools-0.1.19/samtools tview V1.f64.bam genome.fasta

cd /home/train/06.reads_aligment/hisat2
samtools sort -@ 4 -o A.bam -O BAM A.sam 
samtools index A.bam 
samtools faidx genome.fasta 
/opt/biosoft/samtools-0.1.19/samtools tview A.bam genome.fasta
samtools view -b -f 64 A.bam > A.f64.bam
samtools index A.f64.bam
/opt/biosoft/samtools-0.1.19/samtools tview A.f64.bam genome.fasta