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！！
