如何用c语言读bam文件,【一起学生信】bam文件统计覆盖深度、靶向捕获效率

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.