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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