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Query reagrding somatic variant calling

I had a query regarding variant calling.
I have three tissues from the same patient (Tumor, Non-Tumor, and Blood)
I wanted to identify the somatic variants and distinguish them from the germ-line variants.
How should i go about with the comparison?
1) Call the variants in all the 3 tissues separately using Haplotype caller?
2) Call Tumor and Non-Tumor using Mutect2 and Blood using Haplotype caller?
3) Make 3 ways comparison using Mutect2 with each of the tissues?
Any document/post discussing this would also be helpful!!
Thanks a lot in advance :)


  • akovalskakovalsk Member, Broadie, Moderator admin

    Hi @itigupta24 thanks so much for your question. Could you please clarify the purpose of the blood sample in your experimental design?

    In general, Mutect2 is designed for somatic research, and so is probably more appropriate for your needs than Haplotype caller. Mutect2 uses the normal in the tumor/normal pair to identify germline variants. If your blood sample is also meant as a normal sample, you could run Mutect2 on the tumor/blood pair and see how it compares to running the tumor/normal pair.

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