Replace read groups in a BAM file.This tool enables the user to replace all read groups in the INPUT file with a single new read group and assign all reads to this read group in the OUTPUT BAM file.For more information about read groups, see the GATK Dictionary entry. This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH) (see http://ga4gh.org/#/documentation).
java -jar picard.jar AddOrReplaceReadGroups I=input.bam O=output.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20
INPUT (String) Input file (BAM or SAM or a GA4GH url). Required.
OUTPUT (File) Output file (BAM or SAM). Required.
SORT_ORDER (SortOrder) Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate}
RGID (String) Read Group ID Default value: 1. This option can be set to 'null' to clear the default value.
RGLB (String) Read Group library Required.
RGPL (String) Read Group platform (e.g. illumina, solid) Required.
RGPU (String) Read Group platform unit (eg. run barcode) Required.
RGSM (String) Read Group sample name Required.
RGCN (String) Read Group sequencing center name Default value: null.
RGDS (String) Read Group description Default value: null.
RGDT (Iso8601Date) Read Group run date Default value: null.
RGPI (Integer) Read Group predicted insert size Default value: null.
RGPG (String) Read Group program group Default value: null.
RGPM (String) Read Group platform model Default value: null.