Question: Somatic variant calling mutect2 tumour only
1
gravatar for cellulebioinfobiscem
6 days ago by
cellulebioinfobiscem10 wrote:

Hi,

I have to call somatic variant for mutate sample with no matching normal.

I have read the GATK mutect2 page, but still not understand the tumor only mode..

They call that tumor only mode and say "call on each normal sample in this mode", but I don't have normal, so I don't understand what I should do.

Thanks for any explanation:

"

(ii) Tumor-only mode This mode runs on a single type of sample, e.g. the tumor or the normal. To create a PoN, call on each normal sample in this mode, then use CreateSomaticPanelOfNormals to generate the PoN.

  gatk Mutect2 \
   -R reference.fa \
   -I sample.bam \
   -O single_sample.vcf.gz

To call mutations on a tumor sample, call in this mode using a PoN and germline resource. After FilterMutectCalls filtering, consider additional filtering by functional significance with Funcotator.

  gatk Mutect2 \
  -R reference.fa \
  -I sample.bam \
  --germline-resource af-only-gnomad.vcf.gz \
  --panel-of-normals pon.vcf.gz \
  -O single_sample.vcf.gz

"

mutect2 snp gatk • 68 views
ADD COMMENTlink modified 5 days ago by benformatics1.2k • written 6 days ago by cellulebioinfobiscem10
0
gravatar for benformatics
5 days ago by
benformatics1.2k
ETH Zurich
benformatics1.2k wrote:

Your question is confusing... (ii) clearly provides you a command to run (-I can be any sample).

  gatk Mutect2 \
   -R reference.fa \
   -I sample.bam \
   -O single_sample.vcf.gz

The reason there are no explanations on how to do an analysis without a normal/control sample is because frankly you should never do this. They (the GATK team) are not going to provide you with instructions on doing something that they don't think will provide strong results. Nonetheless, you can still run the command as provided.

Relevant GATK forum posts:

ADD COMMENTlink modified 5 days ago • written 5 days ago by benformatics1.2k
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