About GATK Joint call
It is convenient to compare different samples or sample under different candition in one group by GATK Joint call. For one particular sample, could I put WES, WGS, RNASeq bam file together in one group to joint call either two or three types of data in GATK? My thought is that the mutation pattern/distribution for WES and WGS are different, so it might be better not put different types of data together. However, since WES and RNASeq all capture mutation in exon region, could we joint call mutation from WES and RNASeq bam file together? I'm looking forward to your comments.