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  • Comparison of 2 tumor samples

    I have exome data of a study where I have multiple tumor biopsies from one patient, but no normal control.
    I would like to compare the tumor biopsies for mutational similarities and differences. An additional problem is that coverage in some samples is low.

    With my current analysis pipelines I generate vcf files (using mpileup/Varscan2, or MuTect2) of all tumor biopsies seperate. Then I tried to compare the vcf files. The problem now is that if a certain variant is detected in one tumor biopsy but not detected in another I don't know if the variant was not present at all in the 'missed' tumor or was not detected because of bad coverage. Now I have to check all 'missed' variants for coverage depth in the corresponding samples.

    What is a better way to automate/speed up my comparison analysis?

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