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Target Reads // Number of reads covered target region (specified by bed file). Fraction of MapQ reads in mapped reads // Ratio of reads with higher or equal Q score against mapped reads. Fraction of MapQ reads in all reads // Ratio of reads with higher or equal Q score against raw reads. MapQuality above cutoff reads // Number of reads with higher or equal quality score than cutoff value. default is 20, because some variants caller like GATK only consider high quality reads. Map quality cutoff value // Cutoff map quality score, this value can be set by -q. Fraction of PCR duplicate reads // Ratio of PCR duplications. PCR duplicate reads // PCR duplications. backward strand reads // Number of backward strand reads. forward strand reads // Number of forward strand reads. Read2(rmdup) // Mate reads after remove duplications. Read1(rmdup) // First reads after remove duplications. Read1 // First reads in mate paired sequencing Read and mate map to diff chr // Read and mate read mapped to different chromosome, usually because mapping error and structure variants. Singletons // Read mapped but mate read unmapped, and vice versa. Fraction of Read and mate paired // Ratio of read and mate paired against mapped reads Read and mate paired // Read (read1) and mate read (read2) paired. Fraction of Properly paired // Ratio of properly paired reads against mapped reads

Properly paired // Paired reads with properly insert size. Fraction of Mapped Data(Mb) // Ratio of mapped data against raw data. Mapped Data(Mb) // Mapped data in the bam file(s). Fraction of Mapped Reads // Ratio of mapped reads against raw reads. Raw Data(Mb) // Total reads data in the bam file(s). QC Fail reads // Reads number failed QC, this flag is marked by other software,like bwa. Raw Reads (All reads) // All reads in the bam file(s). This file contains all the coverage information of target andįlank region, and reads stat information of the input file(s). Seven files will be created in the output direction. Use rmdup depth instead of cover depth to calculate the coverage of target regions and use_rmdup (an invalid parament since v1.0.0 ) Set this cutoff value for calculate the bad covered region. Default is 0.įor bad mapped paired reads, the inferred insert size is very huge. To show the specified coverage in the coverage.report file.

These unnormal depths in cumulation distrbution file, set the cutoff value to filter them.įor some projects, people care about the coverage of specified depth, like 10000x etc.īamdst just calculate the coverage of 0x, 4x, 10x, 30x, 100x, so you can set this value If you want calculate the coverage of flank region, set this value, default is 200įor some projects, the depths of sepcial region are very high, if you don't want show The probe or captured target region file, these regions will be merged first OPTIONAL PARAMETERS Samtools view in1.bam -u | bamdst -p x.bed -o.