Target Counts Stage

Target counts should be performed for all your samples, whether they are to be used as references or are the case samples under investigation. The case sample and all samples to be used as a panel of normals sample must have identical intervals and therefore should be generated with identical settings. The target counts stage also performs GC Bias correction, which is enabled by default.

The examples below are for WGS processing. For exome processing, see Whole Exome.

The following is an example command for processing a CRAM file.

dragen \
-r <HASHTABLE> \
--cram-input <CRAM> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-map-align false \
--enable-cnv true