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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 https://github.com/samtools/bcftools/issues/40 for further details.