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.
Is it possible to suppress the NON_REF tag on variant calls?
In GVCF output from HaplotypeCaller, each line contains the allele, including the lines with explicit variant calls. Is there a simple way to suppress the allele on variant calls?
Also, what is the reason to have a allele on a variant where a specific alternate allele is called?
Thanks for your help.