We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Gender sensitive

Hi there,

I'm Lynn. I have a question.
Currently, we are doing the annotation and alignment for whole human genome using GATK tools. But we noticed that the chrY is still appeared even the sample is female. When we do the downstream analysis, (eg.:snpeff) the output still shows the chrY in the female subject.

We wonder how can we exclude the chrY and only get the chrX for female samples. Is there any specific command that we need to put in the command line?

Many thanks!


Best Answers


  • AzlinAzlin Member

    Hi @Sheila

    Thank you for your help. :smiley:

  • AzlinAzlin Member

    Hi @Sheila,

    I put the command like this:

    [email protected]:/media/promise/storage/Tools/Softwares/GenomeAnalysisTK-3.4-0$ java -Xmx4g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator --excludeIntervals -XL chrY -R /media/promise/storage/References/Referance/GATK\ Bundle/hg19/ucsc.hg19.fasta -o /media/promise/storage/Postgrad/Deep\ and\ median\ coverage/Deep\ coverage/New\ SM46\ (-XL)/Alignment/SM46.marked.bam.list -o /media/promise/storage/Postgrad/Deep\ and\ median\ coverage/Deep\ coverage/New\ SM46\ (-XL)/Alignment/SM46.marked.bam

    but the ERROR that appeared was:

    ERROR A USER ERROR has occurred (version 3.4-0-g7e26428):
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR MESSAGE: Argument '--excludeIntervals' requires a value but none was provided
    ERROR Argument '--excludeIntervals' requires a value but none was provided
    ERROR ------------------------------------------------------------------------------------------

    it says that --excludeIntervals requires a value but none was provided.
    I want to exclude only chrY in my sequence.

    How can I fix this problem?

    Thank you.

  • AzlinAzlin Member

    Thank you @sheila

    You helped a lot.

    Really appreciate it :smiley:

  • AzlinAzlin Member


    Hi there! It's me again.

    I have read the gatk guide on gatk websites; https://www.broadinstitute.org/gatk/guide/article?id=4133. I just want to double confirm that I only need to add -XL chrY in the command line for RealignerTargetCreator, and BaseRecalibrator steps only right?

    I don't have to include -XL chrY in the command for IndelRealigner and PrintReads steps isn't? Right me if I'm wrong.

    Thank you in advance @Sheila :)

  • AzlinAzlin Member

    Thank you @Sheila :)

    Your kindness is highly appreciated! :):)

Sign In or Register to comment.