Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

How can the difference between Mutect2 FORMAT fields FAD, F1R2, F2R2, SB and AD be explained?

Answered
0

2 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi Eva König,

    Thank you for your question!

    AD and SB are a read based annotations while FAD, F1R2, and F1R2 are fragment based annotations. Fragment counting does not double count paired reads that overlap. So if your paired reads never overlap, the numbers will be equal and if your paired reads always overlap, the fragment counts will be half the read counts. In most situations, some reads overlap but not all.

    Let me know if you have any further questions.

    Best,

    Genevieve

    1
    Comment actions Permalink
  • Avatar
    Eva König

    Thank you Genevieve Brandt (she/her) your answer was very helpful.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk