Raw Reads (All reads) are a bit off

[cangfengzhe]

bamdst is a good tools, but it has a bit problems.
Raw Reads (All reads) is equal to the result of samtools view $bam | wc -l , not the number of fastq reads. Maybe it Ignored the supplementary alignment.So is the Raw Data(Mb)

[shiquan]

Sorry for the later reply. What aligner did you use? I think this difference comes from the aligner skip some reads in default. samtools view $bam | wc -l will output all the bam records including primary and secondary alignments. But in theory, secondary alignments should not be counted, because the primary alignments are already considered.

[ray1919]

I found "Fraction of Mapped Reads" different from samtools result. It is cause by "Raw Reads (All reads)" stats.

[shiquan]

@ray1919 Can you try to use samtools flagstat to confirm this. There might be some different due to secondary alignments.

[ray1919]

samtools flagstat

114102 + 0 in total (QC-passed reads + QC-failed reads)
81904 + 0 primary
0 + 0 secondary
32198 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
110519 + 0 mapped (96.86% : N/A)
78321 + 0 primary mapped (95.63% : N/A)
81904 + 0 paired in sequencing
40318 + 0 read1
41586 + 0 read2
50248 + 0 properly paired (61.35% : N/A)
76756 + 0 with itself and mate mapped
1565 + 0 singletons (1.91% : N/A)
26178 + 0 with mate mapped to a different chr
4050 + 0 with mate mapped to a different chr (mapQ>=5)

bamdst report top 10 line:

## The file was created by bamdst
## Version : 1.0.9
## Files : PC00253-P1-591_dedup.bam 
                               [Total] Raw Reads (All reads)	114102
                                       [Total] QC Fail reads	0
                                        [Total] Raw Data(Mb)	11.95
                                        [Total] Paired Reads	81904
                                        [Total] Mapped Reads	78321
                            [Total] Fraction of Mapped Reads	68.64%
                                     [Total] Mapped Data(Mb)	10.10

bamdst:

$$[Total] Fraction of Mapped Reads = [Total] Mapped Reads / [Total] Raw Reads (All reads)$$

samtools:

primary mapped % = primary mapped / primary

They are somewhat different.