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Is number of samples = 30 enough for variant calling ?
I have 90 exome samples coming from three sample groups. What would be the best idea to do variant calling using GATK? I am planning to call variant from three sample groups separately and and compare them. So, per group there are 30 samples; is this number of sample suffecient enough to merge BAM files and call variants ?
I also have RNASeq data from the same samples. Is it good idea to call variants from RNASeq data too ?