PanDepth快速计算reads深度，覆盖度

计算reads的覆盖度经常使用samtools，但是pandepth的速度会更加快！

PanDepth安装非常简单

wget -c https://github.com/HuiyangYu/PanDepth/releases/download/v2.21/PanDepth-2.21-Linux-x86_64.tar.gz
tar zvxf PanDepth-2.21-Linux-x86_64.tar.gz
cd PanDepth-2.21-Linux-x86_64
./pandepth -h

使用方法也很容易

Usage: pandepth -i in.bam [-g gene.gff|-b region.bed] -o outPrefix
 Input/Output options:
   -i    <str>     input of bam/cram file
   -o    <str>     prefix of output file
 Target options:
   -g    <str>     input gff/gtf file for gene region
   -f    <str>     gff/gtf feature type to parse, CDS or exon [CDS]
   -b    <str>     input bed file for list of regions
   -w    <int>     windows size (bp)
   -a              output all the site depth
 Filter options:
   -q    <int>     min mapping quality [0]
   -x    <int>     exclude reads with any of the bits in FLAG set [1796]
 Other options:
   -t    <int>     number of threads [3]
   -r    <str>     reference genome file for cram decode or GC parse
   -c              enable the calculation of GC content (requires -r)
   -h              show this help [v2.21]

• -g; gff作为输入，可计算基因的深度和覆盖度，配合-f参数使用
• -b; bed 作为输入，计算特定区域的深度和覆盖度
• -w；也可以设置窗口进行计算

计算结果

#Chr    Start   End     RegionID        Length  CoveredSite     TotalDepth      Coverage(%)     MeanDepth
Chr1    111000000       114000000       Chr1_111000000_114000000        3000001 2998433 41785852        99.95   13.93
Chr3    62000000        65000000        Chr3_62000000_65000000  3000001 2998535 38989970        99.95   13.00
Chr5    59000000        61000000        Chr5_59000000_61000000  2000001 1998879 26274524        99.94   13.14
Chr5    97000000        98600000        Chr5_97000000_98600000  1600001 1599186 22561142        99.95   14.10
Chr5    104000000       107000000       Chr5_104000000_107000000        3000001 2998600 45667305        99.95   15.22
Chr6    66000000        78000000        Chr6_66000000_78000000  12000001        11994137        164662023       99.95   13.72
##RegionLength: 24600006        CoveredSite: 24587770   Coverage(%): 99.95      MeanDepth: 13.82

覆盖度和深度都可以显示，非常的方便，主要是速度够快！！