Enable SelectVariants to drop specific annotation fields when subsetting a callset

[vdauwera]

Feature request

Tool involved: SelectVariants

Description

When subsetting a few samples from a large callset, many annotation fields become irrelevant clutter. These can be removed post-hoc but it would be great to be able to just remove them during the subsetting operation. The syntax for specifying what to drop could be similar to the syntax for selecting fields to extract using VariantsToTable. For example, I could do:

gatk SelectVariants -V my.vcf -O subset.vcf -sn MySampleName -DF some_info_annot -DGF some_genotype_annot 

Where -DF / --drop-field and -DGF / --drop-genotype-field lead to the resulting VCFs not having those annotation fields anymore (ie they are removed from all records and from the header).