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Hello everyone,
I have used GATK to call snp in a pair of cancer and normal samples, and obtained the final filtered snp.vcf file. I want to sort out cancer-specific snps, those snps existent only in cancer tissue, does anyone have the command line to achieve this? the GATK team suggested SelectVariants to me, does anyone have the command line to extract cancer-specific snps using SelectVariants? Thank you so much for your reply.
I have used GATK to call snp in a pair of cancer and normal samples, and obtained the final filtered snp.vcf file. I want to sort out cancer-specific snps, those snps existent only in cancer tissue, does anyone have the command line to achieve this? the GATK team suggested SelectVariants to me, does anyone have the command line to extract cancer-specific snps using SelectVariants? Thank you so much for your reply.