Service Notice: Due to the blizzard currently hammering the US Northeast, the Broad is shut down and the GATK forum will be mostly unattended while we hunker down and sip hot cocoa with marshmallows. Assuming the power stays on and we're able to dig ourselves out of the snow when it's all over, normal service should resume Wednesday or Thursday.


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

Sign In or Register to comment.