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Using GATK to compare allele frequencies between 2 cohorts

gilbygilby londonMember

I have RNAseq data for 2 groups of 4 individuals that are phenotypically different. My hypothesis is that some of the genes that show differential expression between the two groups could be due to the presence of snps in exons. Using the RNAseq data, is it possible to use gatk to find differences in snps between these two groups?

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