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Somatic mutations of epithelial cells (HaplotypeCaller vs Mutect)

firadazerfiradazer United KingdomMember
edited February 2017 in Ask the GATK team

Hello, I'd like to extract somatic mutations from normal epithelial cells of cancer patients.

And it's confusing which tool to use. HaplotypeCaller or Mutect?

I know Mutect is for calling somatic mutations but the data is not about cancer cells.

Mutect is different from HaplotypeCaller because it is not based on diploid calculation.

Cancer cells are usually not diploid, so Mutect is useful in that case. (Is this correct?)

But I'm dealing with epithelial cells, so if reads don't show as diploid, then it's presumably sequencing error.

i.e.,
ref: A
reads: AAACCCGGG

In the case above, it seems like triploid, so Mutect will detect the base pair as somatic variant while HaplotypeCaller might not call it as a variant.

Again, I'm using normal epithelial cells, not cancer cells. So it should be diploid.

Should I use HaplotypeCaller or Mutect?

Do you also think that removing all the variants which already exist in dbsnp database from results of HaplotypeCaller is a correct process for getting somatic mutations from normal epithelial cells?

Issue · Github
by Sheila

Issue Number
1732
State
closed
Last Updated
Assignee
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Milestone
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Closed By
sooheelee

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Answers

  • firadazerfiradazer United KingdomMember

    Thank you for your answer and the nice videos, shlee.

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