Hi,
Just like we have FastQC for QC of WGS and exome-data, is there a tool for QC of targeted-gene panel studies? The reason I ask is because some of the metrics from FastQC such as GC content may not hold for a small region captured in a focused NGS panel.

Thanks!

Check out CollectHsMetrics in Picard

https://broadinstitute.github.io/picard/picard-metric-definitions.html#HsMetrics