Fixes the NM, MD, and UQ tags in a SAM file. This tool takes in a SAM or BAM file (sorted by coordinate) and calculates the NM, MD, and UQ tags by comparing with the reference.This may be needed when MergeBamAlignment was run with SORT_ORDER different from 'coordinate' and thus could not fix these tags then.
java -jar picard.jar SetNmMDAndUqTags I=sorted.bam O=fixed.bam \
INPUT (File) The BAM or SAM file to fix. Required.
OUTPUT (File) The fixed BAM or SAM output file. Required.
IS_BISULFITE_SEQUENCE (Boolean) Whether the file contains bisulfite sequence (used when calculating the NM tag). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}