Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Realigner target creator error

HomaHoma Posts: 7Member


I am using Realigner target creator of GATK toolbox but it keeps on giving me this error:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.3-6-gebbba25):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
** ERROR MESSAGE: SAM/BAM file Sample_27.sorted.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups**
ERROR ------------------------------------------------------------------------------------------

How could I solve this problem.

Thanks a lot in advance.

Sign In or Register to comment.