The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Using GATK to compare allele frequencies between 2 cohorts
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?