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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
BSD 3-Clause "New" or "Revised" License
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why no heterozygous site #3

Closed huangl07 closed 8 months ago

huangl07 commented 8 months ago

Dear,

I have already test the deepsomatic to run both illumina and pacbio platform

but I have find a ambiguous result that all Pass variant is no heterozygous site ,the Pass variant is all homozygous

I wander why

pichuan commented 8 months ago

Hi @huangl07 ,

DeepSomatic calls somatic variants. Unlike germline variants, there isn't really a notion of heterozygous variants. Anything 1/1 by DeepSomatic means it's determined as a somatic variant.

Hope this helps! Feel free to follow up if you have more questions.

huangl07 commented 8 months ago

well，Maybe it difficult to adapt other softwares，I have used sentieon and GATK，they put somatic variant Genotype "0/1"

and Also，it output the normal sample genotype and depth

thankyou！

kishwarshafin commented 8 months ago

Hi @huangl07 ,

If you want to obtain the genotype of the normal, currently the solution would be to run DeepVariant (https://github.com/google/deepvariant) on the normal bam and get the accurate genotypes.

I can lay out two things which prevented us from genotyping the normal:

  1. The truth set comes from SEQC2 which only has Tumor/Normal status, it does not have normal genotypes present.
  2. The intention of somatic calling is to determine normal vs tumor, genotyping the normal variants is a secondary function and there are currently methods like DeepVariant available to do it accurately.

On somatic variants being "0/1" or "1/1": somatic variants generally do not have "genotypes" as they are not inherited, so calling them "0/1" or "1/1" would be synonymous. You can use bcftools to convert all '1/1to '0/1 and vice versa and it should be synonymous. Hope this helps.

huangl07 commented 8 months ago

thankyou!

I will back if I have other questions

kishwarshafin commented 8 months ago

Thank you, I will close this for now. Feel free to re-open if you have more questions.