Multiqc: Illumina DRAGEN On-Premise

[pellonen]

Tool Details

• Name of tool: Dragen Bio-it on-premise
• Tool homepage: https://emea.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html#learn-more-onprem
• Tool description: accelerated software/hardware package for alignment & variant calling
  Dragen Enrichment, Dragen Germline, Dragen RNA pipe, Dragen Somatic pipe

• Data suitable for MultiQC plot(s): GATK/SAMTOOLS equivalents
• Most interesting data for General Stats table: SAMTOOL equivalents

Demo data available in BaseSpace, RNA example:
https://basespace.illumina.com/s/LucXlKME2uYC
Thanks, -pekka

[ewels]

I can't use the crappy BaseSpace downloader tool because it won't ask MacOS Catalina for permission to access the disk properly, so it says that I have 0 bytes available.

If you can download the log files locally, could you please make a pull-request to https://github.com/ewels/MultiQC_TestData with them please? (in a folder data/modules/dragen).

Thanks!

[ewels]

(not big BAM files etc, but all log files is fine)

[pellonen]

Hi,

Sorry, haven’t had time for this. Is this still relevant? Met John Wilson today at FIMM, he was presenting Dragen here, great stuff!

Pekka

[ewels]

I can't write the module without example data, and I can't currently download the example data myself.. So this issue will be on hold until I can get a copy.. :)

Looking forward to hearing more about it in person!

[vladsaveliev]

Hi @ewels, we are started evaluating Dragen as well, and I was looking up if there is is a MultiQC module for it, so ended up here :) Attaching an example output for tumor/normal alignment and variant calling Dragen pipeline.

T_SRR7890936_50pc.tar.gz

I'm gonna take look if I can write up a module for this pipeline. I don't have an example for RNA yet - that's gonna be next.

Vlad

[ewels]

Ok fantastic! Thanks @vladsaveliev, looking forward to it..

[vladsaveliev]

Created a pull request, initiated the module with the support of tumor/normal variant calling pipeline: reporting on mapping metrics similar to samtools stats, coverage stats similar to mosdepth and qualimap bamqc, variant calling QC, runtime metrics, fragment size metrics and ploidy estimation.

[ewels]

Finished in #1098