To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at



Last Active
Member, Broadie, Moderator


  • wshzxcc

    Dear bhandsaker,I have some question about the background population.
    As we all know:To run discovery or genotyping on a single sequenced genome or a small set of genomes, you need to call your data against a background population, such as a set of genomes from the 1000 Genomes Project. The background population does not need to be matched to the target individuals.

    My doubt are as follows:
    How could I use the background population? If I hava a single sequenced genome sample (named: Sample AA),and I have 20 background sample.I did not find the parameter for the background population. I only know the parameter (- I) for the input bam file for target sample AA. Thank you very much

    January 30
  • bhandsaker earned the First Answer badge.
    Answering questions is a great way to show your support for a community!
    January 30
  • bhandsaker earned the 5 Answers badge.
    Your willingness to share knowledge has definitely been noticed.
    January 30
  • bhandsaker earned the 25 Answers badge.
    Looks like you’re starting to make a name for yourself as someone who knows the score!
    January 30
  • bhandsaker earned the 50 Answers badge.
    Why use Google when we could just ask you?
    January 30
  • bhandsaker earned the 100 Answers badge.
    Admit it, you read Wikipedia in your spare time.
    January 30