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Can I use GATK to select a private SNP from multi sample VCF file
Can I use GATK to select a private SNP from multi sample VCF file?
With a private SNP I mean a SNP where all but 1 sample in a multi sample vcf file are genotype 0/0.
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Answers
Yes! See the Workshop slides on this with detailed instructions: broadinstitute.org/gatk//events/2038/GATKwh0-BP-8-Variant_analysis.pdf
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