mrjd utility

[minw2828]

Hello Alexis,

Could you please help add this tool to the CWL workflow if you have not already?
DRAGEN MRJD utility software v1.0

A utility software that replaces the DRAGEN Small Variant Caller output in the homology region of the six medically relevant and challenging genes with MRJD caller output.

Many thanks,
Min

[ohofmann]

Min, can we discuss this? I am reluctant to make changes to the current production workflows (which are frozen until we get accreditation status); and this is something we'd get for free in future DRAGEN updates without the need for making changes now.

[minw2828]

Hi Oliver,

Yes to discuss this. What time would work best for you?

To my knowledge, this is not changing the production workflow. Will need Alexis to confirm.

Sorry, I did not know "this is something we'd get for free in future DRAGEN updates without the need for making changes now."

What I did was to add the --enable-mrjd and --mrjd-enable-high-sensitivity-mode parameters to a feature branch in umccr/cwl-ica.git as Alexis taught me to.

The manual says:

To help user get a single VCF file for downstream anlaysis, we prepared a utility tool that replaces the DRAGEN Small Variant Caller output in the homology region of the six medically relevant and challenging genes with MRJD caller output. The tool also annotates the calls made by MRJD (with "MRJD" tag in the INFO column). Please refer to the DRAGEN Software Support Site page to download the utility tool.

I don't know if this utility tool is already enabled or not. Hence, I open this issue.

I am sorry about the trouble! 🙏

Min