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

Whole genome Pooled sequnce data analysis

0

1 comment

  • Avatar
    Bhanu Gandham

    Hi Tania Zahid

     

    We do not have a pooled samples variant calling pipeline. We think Mutect2 should work since it takes into account probabilistic fluctuations in the proportional coverage, i.e. not assume that exactly X% of reads come from each of the 100/X samples. We have not tested this on our end so please use at your own discretion. 

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk