Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

DepthOfCoverage in GATK4

Hi,
Is there any plan to bring "DepthOfCoverage" tool to GATK4 please?
If yes, when? If No, how can I run the available tool on GATK3.8-0 on multiple samples? Meaning how can I analyse different samples and get all the reports in the easiest way?
Also, can I use GATK3.8-0 with WDL and cromwell?
Thanks in advance
Nawar

Best Answer

  • bhanuGandhambhanuGandham Cambridge MA admin
    Accepted Answer

    Hi @NawarDalila

    I will have to ask the developers and get back to you about porting DepthOfCoverage to GATK4.
    You can run DepthOfCoverage on GATK3.8-0 on multiple samples by creating creating a list of bams. Example shown below.
    java -jar GenomeAnalysisTK.jar \
    -T DepthOfCoverage \
    -R reference.fasta \
    -o file_name_base \
    -I input_bams.list
    Yes, you can I use GATK3.8-0 with WDL and cromwell.

    Regards
    Bhanu

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    Accepted Answer

    Hi @NawarDalila

    I will have to ask the developers and get back to you about porting DepthOfCoverage to GATK4.
    You can run DepthOfCoverage on GATK3.8-0 on multiple samples by creating creating a list of bams. Example shown below.
    java -jar GenomeAnalysisTK.jar \
    -T DepthOfCoverage \
    -R reference.fasta \
    -o file_name_base \
    -I input_bams.list
    Yes, you can I use GATK3.8-0 with WDL and cromwell.

    Regards
    Bhanu

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @NawarDalila

    I brought this up with the dev team and due to popular demand we are working on creating a new tool like DepthOfCoverage, with improved functionalities. I wanted to keep you posted that we have not forgotten about this and we are working on it.
    Thank you.

    Regards
    Bhanu

  • Thank you very much @bhanuGandham. This is great news. I will be excited to see it happening. Please do keep us posted.
    Have a nice day
    Nawar

Sign In or Register to comment.