统计比对率

• 新建文件夹

mkdir flagstat

• 构建脚本前文件

ls *.bam > flagstat_bam
find *.bam>bam_sample
sed -i "s/.sort.bam/ /g" bam_sample
paste flagstat_bam bam_sample >flagstatbam_list

• 构建脚本

vim flagstatbam.sh

cat flagstatbam_list |while read id
do
          arr=(${id})
         bam=${arr[0]}
         sample=${arr[1]}
         samtools flagstat $bam > flagstat/$sample.flagstat.txt &
         done

• 激活并运行脚本

chmod a+x flagstatbam.sh
nohup ./flagstatbam.sh

进入结果文件夹提取所需内容

cat * > flagstat
grep "0 mapped" flagstat  > flagstats
cat flagstats | awk '{print $5}' > flag
sed -i "s/(/ /g" flag
sed -i "s/%/ /g" flag
cat flag