Test-drive the GATK tools and Best Practices pipelines on Terra
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How to view only the variants that are present in multiple MuTect VCF files?
I have several vcf files generated by MuTect comparing tumor to matched normal samples. Is there a way to generate a list or vcf file of the variants that are present in all or many of the samples? Something along the lines of: "these variants are in all of the samples," or "these variants are shared in 2 samples" and so on.
I tried vcf-isec on the MuTect vcf files, but I received a warning about the column names not matching (i.e. 1-Normal and 1-Tumor) and the output file was 28 bytes of unreadable characters.
Any help is appreciated, thank you.