5.5 identifyIlluminaReadGroups - Reassigning read groups based on the platform unit in their name
identifyIlluminaReadGroupsensures that each read’s assigned read group is consistent with its Illumina platform unit. For Illumina data, the platform unit appears at the beginning of the read name (the query template name), and the same platform unit is also recorded in the BAM header for each read group. This task compares the platform unit encoded in the read name with the platform unit associated with the read’s read group. If they do not match, the read group is updated so that the read is assigned to the correct Illumina read group. More information regarding read groups can be found here.
Input
Required inputs :
--bam Input_bam_file.bam |
Input BAM file |
Optional inputs :
None
Specific parameters :
Engine parameters that are common to all tasks can be found here.