The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
BQSR and MD fields
The GATK indel realigner appears to not write an MD field in realigned BAM file entries. I wonder how the base quality score recalibration
program deals with these entries. Does it consider them to be ambiguous and so ignore them, or does it use include them, using the
reference sequence to identify SNPs?