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

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