vcfanno: issues to annotate VCF with gnomAD r3.0
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Entering edit mode
19 months ago

Hi,

I want to annotate a vcf using vcfanno and gnomAD v3 vcf.

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=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#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=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=GNOMAD_V3_AC,Number=1,Type=String,Description="calculated by self of overlapping values in field AC from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_AC_NFE,Number=1,Type=String,Description="calculated by self of overlapping values in field AC_nfe from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_AF,Number=1,Type=String,Description="calculated by self of overlapping values in field AF from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_AF_NFE,Number=1,Type=String,Description="calculated by self of overlapping values in field AF_nfe from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_AN,Number=1,Type=String,Description="calculated by self of overlapping values in field AN from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_AN_NFE,Number=1,Type=String,Description="calculated by self of overlapping values in field AN_nfe from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##INFO=<ID=GNOMAD_V3_ID,Number=1,Type=String,Description="calculated by self of overlapping values in field ID from gnomad.genomes.r3.0.sites.chr1.vcf.bgz">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#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

vcfanno gnomAD • 1.1k views
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Entering edit mode

I think you should add that edit as an answer and accept it instead oof editing the title of the post.

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Ok. I've just done it ;)

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Entering edit mode
19 months ago

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

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