I am looking for any bioinformatics tool that might detect RNA contamination in DNA data (specifically exome data). Although RNA contamination is rare it's something we'd like to study on our samples nonetheless.
Edit: some ideas:
check for rRNA contamination, something like Picard's
CollectRnaSeqMetrics, maybe after mapping with a splice aware aligner and filtering reads that span a junction first.
CollectGcBiasMetricstool. while this won't give me a definitive contamination percentage, a contaminated sample may show differences against other samples that do not have significant RNA contamination.