[靶向捕获]统计bam文件的靶向捕获率等信息
下载bamdst软件,地址:https://github.com/shiquan/bamdst
下载zip文件上传到linux服务器,执行make,就进行编译了,最后生成一个可执行文件bamdst。
执行命令:
./bamdst -p n2.bed -o ./ zjn-1.sort.bam
生成coverage.report,chromosomes.report等文件。
报告示例:
## The file was created by bamdst
## Version : 1.0.9
## Files : xxx.bam
[Total] Raw Reads (All reads) 13208614
[Total] QC Fail reads 0
[Total] Raw Data(Mb) 1981.29
[Total] Paired Reads 13208614
[Total] Mapped Reads 13198598
[Total] Fraction of Mapped Reads 99.92%
[Total] Mapped Data(Mb) 1979.79
[Total] Fraction of Mapped Data(Mb) 99.92%
[Total] Properly paired 12882158
[Total] Fraction of Properly paired 97.53%
[Total] Read and mate paired 13189774
[Total] Fraction of Read and mate paired 99.86%
[Total] Singletons 8824
[Total] Read and mate map to diff chr 126564
[Total] Read1 6604307
[Total] Read2 6604307
[Total] Read1(rmdup) 6602581
[Total] Read2(rmdup) 6596017
[Total] forward strand reads 6600701
[Total] backward strand reads 6597897
[Total] PCR duplicate reads 0
[Total] Fraction of PCR duplicate reads 0.00%
hg38转换hg19参考基因组:
参考: