PanDepth

快速高效计算覆盖度的工具，支持long reads、short reads输入以及bam、cram格式，多线程加速效果较好，同样的CPU线程相比samtools等工具快很多，并且使用cram作为输入数据，速度比bam快。

代码库：https://github.com/HuiyangYu/PanDepth/

安装¶

直接下载编译好的二进制文件

$ 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

集群上调用

$ module load PanDepth/2.21

基本使用¶

所有选项，可以使用-g gene.gff 或 -b region.bed 来对指定区域计算覆盖度，-t 指定线程数。

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]

使用举例

# 跑完后输出文件为 test1.chr.stat.gz
$ pandepth -i test.bam -o test1 -4 6

$ zcat test1.chr.stat.gz
#Chr    Length  CoveredSite TotalDepth  Coverage(%) MeanDepth
Chr01   332615375   331690145   16945298412 99.72   50.95
Chr02   177319215   176853774   8368043949  99.74   47.19
Chr03   289790774   288837978   14143309698 99.67   48.81
Chr04   248932513   248384761   11741149343 99.78   47.17
Chr05   254874144   253897405   12548725234 99.62   49.23
Chr06   253233553   252488900   11854653791 99.71   46.81
Chr07   266382521   265595425   12873116925 99.70   48.33
Chr08   174326481   173874883   8437159467  99.74   48.40
Chr09   278410012   277664711   13068321410 99.73   46.94

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