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.

Example commands in SelectVariants Tool Doc

KurtKurt Member ✭✭✭

Just FYI,

In the example "Set filtered genotypes to no-call (./.):" in;


The argument for setting flagged GT to null is a typo.

The example has it as


should be



Issue · Github
by Geraldine_VdAuwera

Issue Number
Last Updated
Closed By

Best Answer


  • evansbevansb Member


    I'm using the current (3.4-46-gbc02625) version of GATK and I cannot get the "--setFilteredGtToNocall" flag to work with SelectVariants.

    Here is an example of the command I used, which executed without error:

    java -Xmx2g -jar /usr/local/gatk/GenomeAnalysisTK.jar -T SelectVariants -R /home/ben/2015_BIO720/rhesus_genome/macaque_masked_chromosomes_ym.fasta --variant temp55.vcf -o temp66.vcf --setFilteredGenotypesToNocall

    But when I look for SNPs that should have no call, they have not been replaced:
    grep '154930' temp66.vcf
    chr1 154930 . C . 31.62 LowDCoverage AN=2;DP=1;MQ=37.05;MQ0=0 GT:DP 0/0:1
    chr1 25154930 . G . 30.17 LowDCoverage AN=0;DP=3;MQ=37.00;MQ0=0 GT ./.
    chr1 26154930 . T . 34.23 LowDCoverage AN=0;DP=2;MQ=37.00;MQ0=0 GT ./.

    As you can see, the first SNP at chr1 position154930 did not pass the filter (which I applied using VariantFiltratin) but it still has a genotype call "0/0" instead of no call "./.".

    Am I doing something wrong or is this a bug?


  • evansbevansb Member

    Whoops, the command above should be this, which executes with no error and does not swap the genotype to no call as described above:

    java -Xmx2g -jar /usr/local/gatk/GenomeAnalysisTK.jar -T SelectVariants -R /home/ben/2015_BIO720/rhesus_genome/macaque_masked_chromosomes_ym.fasta --variant temp55.vcf -o temp66.vcf --setFilteredGtToNocall

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Ben,

    Can you please submit a bug report? Instructions are here: http://gatkforums.broadinstitute.org/discussion/1894/how-do-i-submit-a-detailed-bug-report


  • evansbevansb Member

    Your ftp server is currently at the max of 20 users. Can you please provide an alternative way to submit a bug report?

  • evansbevansb Member

    OK it is free now; I uploaded a file called "SetFilteredGtToNoCall.zip"

Sign In or Register to comment.