sambamba flagstat没有Primary Mapped Reads

Log

sambamba flagstat统计结果格式和samtools flagstat不一样，没有Primary Mapped Reads

软件版本

  • samtools 1.18
  • sambamba 1.0.1

问题

samtools flagstat与sambamba flagstat输出格式不一样，sambamba flagstat没有Primary Mapped Reads

结果示例

samtools flagstat

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4350490 + 0 in total (QC-passed reads + QC-failed reads)
3501080 + 0 primary
481096 + 0 secondary
368314 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
4319560 + 0 mapped (99.29% : N/A)
3470150 + 0 primary mapped (99.12% : N/A)
3501080 + 0 paired in sequencing
1750540 + 0 read1
1750540 + 0 read2
3469722 + 0 properly paired (99.10% : N/A)
3470118 + 0 with itself and mate mapped
32 + 0 singletons (0.00% : N/A)
76 + 0 with mate mapped to a different chr
20 + 0 with mate mapped to a different chr (mapQ>=5)

sambamba flagstat

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4350490 + 0 in total (QC-passed reads + QC-failed reads)
481096 + 0 secondary
368314 + 0 supplementary
0 + 0 duplicates
4319560 + 0 mapped (99.29%:N/A)
3501080 + 0 paired in sequencing
1750540 + 0 read1
1750540 + 0 read2
3469722 + 0 properly paired (99.10%:N/A)
3470118 + 0 with itself and mate mapped
32 + 0 singletons (0.00%:N/A)
76 + 0 with mate mapped to a different chr
20 + 0 with mate mapped to a different chr (mapQ>=5)

结论

  • samtools flagstat的primary mapped 等于 sambamba flagstat的mapped - secondary - supplementary
  • samtools flagstat结果：3470150 + 0 primary mapped (99.12% : N/A)
  • sambamba flagstat结果：3470150 = 4319560 - 481096 - 368314