Somatic mutation calling using MuTect2 with blood WGS and tumor WES samples

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HYUN BIN CHO

• January 29, 2024 07:37
• Edited

REQUIRED for all errors and issues:
a) GATK version used: 3.8.1
b) Exact command used: Somatic variant calling using MuTect2 
c) Entire program log: No Error

Hello GATK team,

We are conducting somatic mutation calling following a pipeline from GDC DNA-Seq pipeline which is based on MuTect2 in GATK3. (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/)

As far as I know, when comparing a tumor and matched normal samples, it is normal to use a tumor WES data and a normal tissue WES data.

However, we have tumor WES samples (30x) and matched blood WGS samples (500x). Is it okay to use these pairs of samples for somatic mutation calling without any pre-processing?

We deeply appreciate your support.

Thank you.

 

  

 

 

 

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  David Benjamin

  • January 29, 2024 17:50

  HYUN BIN CHO This will work very well, with no preprocessing needed.  In fact, it will probably help avoid the occasional false positive near low-coverage tails of baited intervals.

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