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.
Cram to Bam Conversion Lost MD:Z Tag (GATK 3.5)
I have been messing around with cram usage within GATK 3.5 and came across a dropped tag when converting from a cram file back to a bam file. Below is how I went about recreating the BAM file.
java -jar gatk-3.5/GenomeAnalysisTK.jar \
-T PrintReads \
-R $REF_GENOME \
-I $CRAM_FILE \
-o $CRAM_FILE"2.bam" \
This is the same way I went about bam -> cram creation and there was nothing lost. Any input or suggestions is greatly appreciated.