samtools软件的使用

常用samtools的命令：

samtools常用命令

• samtools view命令：查看sam，bam文件，进行sam及bam文件的转换

(rna) May5 16:58:12 ~/project/airway/05.mapping
$ samtools view *.subjunc.bam |less -S   #只显示结果部分
(rna) May5 16:58:30 ~/project/airway/05.mapping
$ samtools view -H  *.subjunc.bam |less -S  #只显示结果的表头部分
(rna) May5 16:58:44 ~/project/airway/05.mapping
$ samtools view -h  *.subjunc.bam |less -S  #结果和表头部分都显示
(rna) May5 17:23:53 ~/project/airway/05.mapping
$ samtools view *subjunc.bam | less -S   #查看*subjunc.bam文件（未排序，按照SRR排序）
(rna) May5 17:24:54 ~/project/airway/05.mapping
$ samtools view *subjunc.sort.bam | less -S  #查看*subjunc.sort.bam文件（已按照染色体文字排序，前面为匹配reads，最后为未匹配reads）

• samtools sort 命令

samtools sort -@ 1 -o SRR1039510.hisat2.sort.bam SRR1039510.hisat2.sam  #对SRR1039510.hisat2.sam文件进行排序，线程数（参数-@ ）1，输出SRR1039510.hisat2.sort.bam 文件（进行排序后转换为bam文件）

• samtools index 需要将bam文件排序（上一步），添加索引，才能载入IGV进行可视化

(rna) May5 17:37:46 ~/project/airway/05.mapping
$ for i in $(ls *.sort.bam)
> do
>         i=${i/.sort.bam/}
>         samtools index ${i}.sort.bam
> done
(rna) May5 17:38:50 ~/project/airway/05.mapping
$ ls
SRR1039510_1_val_1.fq.gz    SRR1039510.hisat2.sort.bam.bai       SRR1039510.subjunc.log           SRR1039511_2_val_2.fq.gz
SRR1039510_2_val_2.fq.gz    SRR1039510.subjunc.bam               SRR1039510.subjunc.sort.bam      SRR1039512_1_val_1.fq.gz
SRR1039510.hisat2.sam       SRR1039510.subjunc.bam.indel.vcf     SRR1039510.subjunc.sort.bam.bai  SRR1039512_2_val_2.fq.gz
SRR1039510.hisat2.sort.bam  SRR1039510.subjunc.bam.junction.bed  SRR1039511_1_val_1.fq.gz
#将*sort.bam文件及*sort.bam.bai文件下载到本地，使用igv进行查看

• samtools tview 简易版基因组浏览器，直接可以在命令行下查看基因位置（此命令的输入文件也是要进行排序和建立索引的）

(rna) May5 17:45:21 ~/project/airway/05.mapping
$ hg38=/teach/database/reference/hg38.fa   #建立索引，即目录
(rna) May5 17:47:48 ~/project/airway/05.mapping
$ samtools tview SRR1039510.hisat2.sort.bam ${hg38}  #samtools tview命令进入交互式的界面，输入？查看帮助，输入g可输入染色体编号及位置可查看reads比对的情况

• samtools flagstat # 比对结果的统计

(rna) May5 18:13:39 ~/project/airway/05.mapping
$ samtools flagstat  #打开帮助文档
Usage: samtools flagstat [options] <in.bam>
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -@, --threads INT
               Number of additional threads to use [0]
(rna) May5 18:15:48 ~/project/airway/05.mapping
$ samtools flagstat -@ 1 *.hisat2.sort.bam  #根据帮助文档设置参数及输入文件
54530 + 0 in total (QC-passed reads + QC-failed reads)  #结果
5634 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
53767 + 0 mapped (98.60% : N/A)
48896 + 0 paired in sequencing
24448 + 0 read1
24448 + 0 read2
47108 + 0 properly paired (96.34% : N/A)
47564 + 0 with itself and mate mapped
569 + 0 singletons (1.16% : N/A)
200 + 0 with mate mapped to a different chr
145 + 0 with mate mapped to a different chr (mapQ>=5)