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.