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

Per-sample SimulateReadsForVariants

Dear list,

I would like to better understand how the module SimulateReadsForVariants is working with VCF files.

Given a VCF file containing 10 samples, I expected the SimulateReadsForVariants to simulate 10 BAM files for each sample. The module however simulates only 1 BAM file.

How can we generate sample-specific simulated BAM files?

Do we have to create 10 VCF files containing only 1 sample each?

Many thanks for your lights,



Best Answers


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Rémi,

    I'll have to check the code for the expected behavior of the tool, but in the meantime, can you check your bam file and let me know whether there are different read groups defined in the header, or whether there's just one?

Sign In or Register to comment.