Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

what it means the NO CALL from GATK

ibseqibseq United KingdomMember

Hi all,
just curious to know what exactly means that for certain SNPs we read ""NO CALL" on our vcf file, despite not been filtered out?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited May 2018

    Hi Irene,

    ./. or no-call genotypes occur when the tool does not have enough information to make a proper genotype call. This could be due to low coverage or bad quality data or messy regions in general.


Sign In or Register to comment.