Generate an Alignment File

The following command line examples show how to run the DRAGEN map/align pipeline depending on your input type. The map/align pipeline generates an alignment file in the form of a BAM or CRAM file that can then be used in the DRAGEN CNV Pipeline.

You need to generate alignment files for all samples that have not already been mapped and aligned, including any samples to be used as references for normalization. Each sample must have a unique sample identifier, which is specified with the --RGSM option. For BAM and CRAM input files, the sample identifier is taken from the file, so the --RGSM option is not required.

Example command to map/align an existing BAM file:

dragen \
-r <HASHTABLE> \
--bam-input <BAM> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-map-align true

Example command to map/align an existing CRAM file:

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