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Haplotype GVCF mode

wi24wi24 PhiladeplhiaMember
Hi

I have question about if a) I should run haplotype caller in single sample mode or b) if I should GVCF mode combining all samples from my study or c) if I should just group all the cases together and all controls together and then run GVCF mode seperately for both groups

I am currently following GATK best practices guideline for germline variant calling.
I am interested in analyzing germline mutations and signatures and all samples are from the same cancer type but divided into two categories: a) either had somatic mutation in my gene of interest and a high somatic mutation burden (cases) or b) no mutation in my gene of interest and low mutation burden (controls).

I am using aligned sequencing reads from blood derived normal for the TCGA data in GDC and using haplotype caller. I have 10 samples in the control and 10 for the cases.

I would appreciate any feedback and or advice and Thank you in advance

Answers

  • wi24wi24 PhiladeplhiaMember
    I wanted to clarify my previous post

    I want to know what defines a cohort to use the Joint-Call cohort? and to Clarify two of my samples in the cases are not from blood derived normal but are from normal tissue instead. However all cases and controls are from the same cancer type (uterine endometrial carcinoma)

    Do I joint-call the controls and joint-call the cases separately, or should I joint-call them all together? What is a cohort?"
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