Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 ?