Question: Hi,

I want to annotate a vcf using [vcfanno](https://github.com/brentp/vcfanno) and [gnomAD v3 vcf](https://gnomad.broadinstitute.org/).

using this conf.toml (here using only chr1 vcf from gnomAD)

[[annotation]]
file="gnomad.genomes.r3.0.sites.chr1.vcf.bgz"
fields = ["AF", "AC", "AN", "AF_nfe","AC_nfe", "AN_nfe", "FILTER", "ID"]
names = ["GNOMAD_V3_AF", "GNOMAD_V3_AC", "GNOMAD_V3_AN","GNOMAD_V3_AF_NFE", "GNOMAD_V3_AC_NFE","GNOMAD_V3_AN_NFE","GNOMAD_V3_FILTER","GNOMAD_V3_ID"]
ops=["self", "self", "self", "self", "self", "self", "self", "self"]

and this test vcf

##fileformat=VCFv4.2
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE_1	SAMPLE_2
chr1	12807	.	C	T	55.5	PASS	AC=20;AF=0.5	GT:AD:DP	0/1:50,100:150	0/0:100,1:101
chr1	4545727	.	C	T	55.5	PASS	AC=30;AF=0.25	GT:AD:DP	1/1:10,100:110	0/1:100,100:200

with this command :

vcfanno_linux64 gnomad_v3_conf.toml test.vcf > test_vcfanno.vcf

It results in :

=============================================
vcfanno version 0.3.1 [built with go1.11]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 8 sources from 1 files
api.go:804: WARNING: using op 'self' when with Number='1' for 'AF' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'AC' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'AN' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'AF_nfe' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'AC_nfe' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'AN_nfe' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'FILTER' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
api.go:804: WARNING: using op 'self' when with Number='1' for 'ID' from 'gnomad.genomes.r3.0.sites.chr1.vcf.bgz' can result in out-of-order values when the query is multi-allelic
api.go:805: : this is not an issue if the query has been decomposed.
vcfanno.go:241: annotated 2 variants in 0.09 seconds (22.9 / second)

resulting VCF didn't contain the gnomAD AF,AC and AN. Only the header has the INFO filed added from gnomAD VCF :

##fileformat=VCFv4.2
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE_1	SAMPLE_2
chr1	12807	.	C	T	55.5	PASS	AC=20;AF=0.5	GT:AD:DP	0/1:50,100:150	0/0:100,1:101
chr1	4545727	.	C	T	55.5	PASS	AC=30;AF=0.25	GT:AD:DP	1/1:10,100:110	0/1:100,100:200

Did I miss something obvious here?
Thanks

Answer: Solved it by updating vcfanno from 0.3.1 to 0.3.2. Now it works ;)