Example commands in SelectVariants Tool Doc

Just FYI,

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

https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

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

The example has it as

--setFilteredGenotypesToNocall

should be

--setFilteredGtToNocall

Tagged:

Issue · Github
by Geraldine_VdAuwera

Issue Number
1159
State
closed
Last Updated
Milestone
Array
Closed By
vdauwera

Best Answer

Answers

  • Hello,

    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?

    Thanks,
    Ben

  • 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

    @evansb
    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

    Thanks,
    Sheila

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

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

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