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.


  • ebanksebanks Broad InstitutePosts: 689Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP admin

    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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