I read about a few other people's posts concerning realigner target creator but felt that my issue couldn't be addressed after trying their approaches. Thus comes this post.
Not sure why I got the error message (see below for details), as I assumed the uploaded files were BAM files, not SAM.
Issue: realigner target creator failed to execute (database build under attribute: Human Feb 2009 (GRCh37/hg19)) Source for the reference list: “History”
Selected reference file: ucsc.hg19.fasta (selecting from the Shared Data the whole GATK bundle, among which ucsc.hg19.fasta is the only one available in the dropdown)
Input file: a BAM file after running SAM-to-BAM conversion (database build under attribute: Human Feb 2009 (GRCh37/hg19))
Run with basic GATK options and basic analysis options.
##### ERROR MESSAGE: SAM/BAM file /galaxy-repl/main/scratch/tmp-gatk-brCFJ1/gatk_input.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
Any suggestion ? Great many thanks.