SystemSystem Posts: 226Administrator admin
edited July 2012 in Tool Bulletin

A new tool has been released!

Check out the documentation at FlagStat.


  • mgujralmgujral Posts: 2Member

    Hi there,

    I have a question related to the output of FlagStat. I used BWA mem with version 0.7.4 to align the reads and following is the output of FlagStat

    1290814928 in total 0 QC failure 0 duplicates 1269372151 mapped (98.34%) 1290814928 paired in sequencing 645318681 read1 645496247 read2 0 properly paired (0.00%) 1264066894 with itself and mate mapped 5305257 singletons (0.41%) 54566084 with mate mapped to a different chr 13502927 with mate mapped to a different chr (mapQ>=5)

    In output,1290814928 paired in sequencing, but 0% are properly paired. What does that mean? What could be reason for 0% properly mapped? I will greatly appreciate your input.

    best, --Madhu

  • ebanksebanks Posts: 684GATK Developer mod

    Hi Madhu,

    The proper pair status is read directly from the SAM record - it's the 0x2 bit in the FLAG field (the second token in a SAM record). See the SAM specification for more details.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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