It is imperative that any sequencing/analysis done at the McDermott Center have the highest standards of data quality. This includes not just sequencing quality statistics, but also experiment quality statistics which are equally important. For this purpose, we use a set of tools that is part of the PICARD tool-set as well as diagnosis tools from GATK.
Good coverage is very important in order to be confident about the variants being called. We check each sample individually to make sure that they meet our minimum thresholds of at least 50x average coverage and 95%-98% over 20x coverage. A per target coverage table is provided as well as a diagram of the percentage bases covered with X coverage.
PICARD provides a host of alignment metrics that can be very useful for experiment quality assessment. We specifically provide the following metrics: