Suggestion: contamination

[husamia]

From my experience. One of the biggest quality issues that can come up and is hard to detect is contamination. The coverage metrics doesn't capture it specifically. If it's at high levels it causes errors that are hard to quantify. such as misalignment and subsequently variant calling. Should it be part of the sample QC metric? I would define contamination as DNA molecules that get sequenced that are not part of the target reference of the human genome. like bacterial DNA that could be introduced during the extraction. the other contamination type could be from other samples.