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I am working on a data set in which (1) multiple individuals were sequenced on the same lane, and (2) the same individuals were sequenced in multiple runs. If I get this right, we would thus want to consider both lane and run as covariates in BQSR. I have two questions related to this:
1) Which elements of the @RG header are considered by BQSR? All given there (e.g. ID, SM, LB, PI, PL)?
2) I am not sure where (in which @RG elemnt) to best incorporate run and lane info?