Separate vcf file creation for matched tumor-normal samples
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7 weeks ago
Gene_MMP8 ▴ 210

I have received 8 matched normal tumor vcf files from our collaborators. For some reason, they didn't provide the sequence bam files and called the variants themselves (by aligning with the reference hg19 genome for both pairs separately). Basically, I have files named x_normal.vcf and x_tumor.vcf (where x=1 to 8). My intention is to call somatic variants for each sample (using Mutect2), convert them to the maf format, and run the MutSigCV tool to identify driver genes.

However, I understand that Mutect2 requires separate bam files for normal tumor pairs (which I don't have). So how do I proceed with my analysis?

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