Open source software for reprocessing WGS samples run by GATK to Dragen

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Mela

• June 25, 2024 21:34

Hi,

Is there any available open source software that we can use to reprocess WGS samples previously ran by GATK? We are hoping to joint call all the previous samples ran by GATK with all the samples ran by DRAGEN.

I hope to get your advice on this. 

Thank you so much.

Mela

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  Gökalp Çelik

  • June 26, 2024 05:41

  Hi Mela

  Do you want to perform all preprocessing steps as well or just do variant calling?

  If you wish to perform all preprocessing steps then Dragmap mapper is available as open source read mapper from 

  https://github.com/Illumina/DRAGMAP

  Beware that the latest update was 2 years ago for this tool therefore it may not behave exactly how it works in the actual dragen hardware you currently have. 

  For the variant calling steps you may need to resort to GATK

  --dragen-mode

  Keep in mind that this mode has its own quirks when it comes to functional equivalence vs maximum quality. You may get more information about those 2 modes from the links below

  https://gatk.broadinstitute.org/hc/en-us/articles/4410456501915-Functional-equivalence-in-DRAGEN-GATK 

  https://broadinstitute.github.io/warp/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README/ 

  Finally make sure that you use the same reference genome as the one used in DRAGEN hardware with the exact same masked regions and reference fasta otherwise you may end up inconsistent results during your joint call steps. 

  I hope this helps.

  Regards. 

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