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Does PrintReads accepts gz bam files ?
I am feeding a list of BAM.gz files into PrintReads to get a subset of BAM files for a region. I get this error message !
ERROR MESSAGE: SAM/BAM/CRAM file BL01.sorted.dedup.rlgn.bam.gz is malformed. Please see http://gatkforums.broadinstitute.org/discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cramfor more information. Error details: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
I do not see any problem with BAM files. the question is can I feed "bam.gz" files into PrintReads ?