Comments (4)
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.
from bamdst.
I found "Fraction of Mapped Reads" different from samtools result. It is cause by "Raw Reads (All reads)" stats.
from bamdst.
@ray1919 Can you try to use samtools flagstat
to confirm this. There might be some different due to secondary alignments.
from bamdst.
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:
samtools:
primary mapped % = primary mapped / primary
They are somewhat different.
from bamdst.
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from bamdst.