Question: No Somatic SNV Calling with GATK?
1
gravatar for sichan
3.6 years ago by
sichan70
Canada
sichan70 wrote:

Hi,

I see that GATK should *not* be used to call somatic variants from tumor/normal pairs:
http://gatkforums.broadinstitute.org/discussion/2405/can-i-use-unifiedgenotyper-to-call-somatic-variants-in-tumor-control-tissues

Is this still true today?  I ask because someone who is no longer in our group generated 'somatic calls' by
* calling SNPs on the normal
* calling SNPs on the matched tumor
* subtracting the normal SNPs from the tumor SNPs

I'm trying to determine how useful those calls are (probably not much).

This post from ~2 years ago also suggests that GATK should not be used for somatic calls:
Difference Between Somatic And Germline Variant Calling?

Thank you.

snp • 1.8k views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 3.6 years ago by sichan70

Thanks everyone!  Yes, I forgot to mention that I had already started running MuTect, which is also from Broad. 

ADD REPLYlink written 3.6 years ago by sichan70

Try to refrain from posting thanks as an answer.  An upvote or accepted answer will do just fine!

ADD REPLYlink written 3.6 years ago by Daniel Swan13k
2
gravatar for Sean Davis
3.6 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You should definitely abandon those calls and use a tool designed for somatic variant calling.  There are numerous tools to choose from.

ADD COMMENTlink written 3.6 years ago by Sean Davis25k
1

You can use MuTect, which is based on GATK and is available for download from the GATK website. 

ADD REPLYlink written 3.6 years ago by vdauwera890
1

Yes, MuTect is one of many and a popular one.  On the downside, it is pretty slow unless one takes the time to run it in parallel.

ADD REPLYlink written 3.6 years ago by Sean Davis25k
1

I could't agree more. This naive subtractive approach is in no way comparable to say VarScan2.

ADD REPLYlink written 3.6 years ago by Daniel Swan13k
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