To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Change format of AD field to Number=R?


In GATK version 3.5 I see the following in VCF headers:

##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

However, the number of values in the AD field should always be the number of alleles (including the reference), right? The 4.2 VCF spec has a value R to represent this. Therefore, could the header line be changed to the following in future GATK releases?

##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

Why is this important? Well, one reason is that bcftools norm uses this when splitting multiallelic variants into multiple biallelics. With the '.' this isn't done correctly, but with the 'R' it is. See the comment from freeseek at for further details.


Issue · Github
by Sheila

Issue Number
Last Updated
Closed By


Sign In or Register to comment.