【一起学生信】bam文件统计覆盖深度、靶向捕获效率

bam文件统计覆盖深度、靶向捕获效率是在基因组测序分析中经常用到的操作，之前也用过python、perl实现过但是速度比较慢，今天偶然发现了一个软件bamdst（https://github.com/shiquan/bamdst)， 采用c语言编写，速度快，分析的类型也比较多，涉及到了mapping统计、靶向捕获统计、flanking区域统计、深度覆盖统计等。

用起来比较方便，具体使用可以参考github。

以下是这个软件分析的项目以及解释。

Item	Annotation
[Total] Raw Reads (All reads)	All reads in the bam file(s).
[Total] QC Fail reads	Reads number failed QC, this flag is marked by other software,like bwa. See flag in the bam structure.
[Total] Raw Data(Mb)	Total reads data in the bam file(s).
[Total] Paired Reads	Paired reads numbers.
[Total] Mapped Reads	Mapped reads numbers.
[Total] Fraction of Mapped Reads	Ratio of mapped reads against raw reads.
[Total] Mapped Data(Mb)	Mapped data in the bam file(s).
[Total] Fraction of Mapped Data(Mb)	Ratio of mapped data against raw data.
[Total] Properly paired	Paired reads with properly insert size. See bam format protocol for details.
[Total] Fraction of Properly paired	Ratio of properly paired reads against mapped reads
[Total] Read and mate paired	Read (read1) and mate read (read2) paired.
[Total] Fraction of Read and mate paired	Ratio of read and mate paired against mapped reads
[Total] Singletons	Read mapped but mate read unmapped, and vice versa.
[Total] Read and mate map to diff chr	Read and mate read mapped to different chromosome, usually because mapping error and structure variants.
[Total] Read1	First reads in mate paired sequencing
[Total] Read2	Mate reads
[Total] Read1(rmdup)	First reads after remove duplications.
[Total] Read2(rmdup)	Mate reads after remove duplications.
[Total] forward strand reads	Number of forward strand reads.
[Total] backward strand reads	Number of backward strand reads.
[Total] PCR duplicate reads	PCR duplications.
[Total] Fraction of PCR duplicate reads	Ratio of PCR duplications.
[Total] Map quality cutoff value	Cutoff map quality score, this value can be set by -q. default is 20, because some variants caller like GATK only consider high quality reads.
[Total] MapQuality above cutoff reads	Number of reads with higher or equal quality score than cutoff value.
[Total] Fraction of MapQ reads in all reads	Ratio of reads with higher or equal Q score against raw reads.
[Total] Fraction of MapQ reads in mapped reads	Ratio of reads with higher or equal Q score against mapped reads.
[Target] Target Reads	Number of reads covered target region (specified by bed file).
[Target] Fraction of Target Reads in all reads	Ratio of target reads against raw reads.
[Target] Fraction of Target Reads in mapped reads	Ratio of target reads against mapped reads.
[Target] Target Data(Mb)	Total bases covered target region. If a read covered target region partly, only the covered bases will be counted.
[Target] Target Data Rmdup(Mb)	Total bases covered target region after remove PCR duplications.
[Target] Fraction of Target Data in all data	Ratio of target bases against raw bases.
[Target] Fraction of Target Data in mapped data	Ratio of target bases against mapped bases.
[Target] Len of region	The length of target regions.
[Target] Average depth	Average depth of target regions. Calculated by "target bases   length of regions".
[Target] Average depth(rmdup)	Average depth of target regions after remove PCR duplications.
[Target] Coverage (>0x)	Ratio of bases with depth greater than 0x in target regions, which also means the ratio of covered regions in target regions.
[Target] Coverage (>=4x)	Ratio of bases with depth greater than or equal to 4x in target regions.
[Target] Coverage (>=10x)	Ratio of bases with depth greater than or equal to 10x in target regions.
[Target] Coverage (>=30x)	Ratio of bases with depth greater than or equal to 30x in target regions.
[Target] Coverage (>=100x)	Ratio of bases with depth greater than or equal to 100x in target regions.
[Target] Target Region Count	Number of target regions. In normal practise,it is the total number of exomes.
[Target] Region covered > 0x	The number of these regions with average depth greater than 0x.
[Target] Fraction Region covered > 0x	Ratio of these regions with average depth greater than 0x.
[Target] Fraction Region covered >= 4x	Ratio of these regions with average depth greater than or equal to 4x.
[Target] Fraction Region covered >= 10x	Ratio of these regions with average depth greater than or equal to 10x.
[Target] Fraction Region covered >= 30x	Ratio of these regions with average depth greater than or equal to 30x.
[Target] Fraction Region covered >= 100x	Ratio of these regions with average depth greater than or equal to 100x.
[flank] flank size	The flank size will be count. 200 bp in default. Oligos could also capture the nearby regions of target regions.
[flank] Len of region (not include target region)	The length of flank regions (target regions will not be count).
[flank] Average depth	Average depth of flank regions.
[flank] flank Reads	The total number of reads covered the flank regions. Note: some reads covered the edge of target regions, will be count in flank regions also.
[flank] Fraction of flank Reads in all reads	Ratio of reads covered in flank regions against raw reads.
[flank] Fraction of flank Reads in mapped reads	Ration of reads covered in flank regions against mapped reads.
[flank] flank Data(Mb)	Total bases in the flank regions.
[flank] Fraction of flank Data in all data	Ratio of total bases in the flank regions against raw data.
[flank] Fraction of flank Data in mapped data	Ratio of total bases in the flank regions against mapped data.
[flank] Coverage (>0x)	Ratio of flank bases with depth greater than 0x.
[flank] Coverage (>=4x)	Ratio of flank bases with depth greater than or equal to 4x.
[flank] Coverage (>=10x)	Ratio of flank bases with depth greater than or equal to 10x.
[flank] Coverage (>=30x)	Ratio of flank bases with depth greater than or equal to 30x.
[flank] Coverage (>=100x)	Ratio of flank bases with depth greater than or equal to 100x.