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

Splitting multiple sample VCF to single sample VCF before VariantFilteration


1 comment

  • Avatar
    Gökalp Çelik

    Hi Are M

    Both approaches are fine and valid for your purpose but in general our team suggests filtering first and splitting later approach. Filtering in multisample VCFs provide better evidence for rare variants therefore it is more preferable. 

    I hope this helps.  

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk