vcfanno output

[Laure Fresard]

Hi, 

I would like to annotate my vcf files with gnomAD allele frequencies.

my conf.toml looks like this:

[[annotation]]

file="mypathto/gnomad.genomes.r2.0.2.sites.chr22.vcf.bgz"

fields = ["AF"]

names=["gnmoAD_AF"]

ops=["self"]

it's running fine but if I do have a new info file in my output file:

##INFO=<ID=gnmoAD_AF,Number=1,Type=String,Description="calculated by self of overlapping values in field AF from "mypathto/gnomad.genomes

.r2.0.2.sites.chr22.vcf.bgz">

I don't have any gnomAD field in my output:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RD048

22 16123164 . C A . PASS GT:VR:RR:DP:GQ 0/1:6:32:38:.

My command line is 

vcfanno -p 2 conf.toml mysample.vcf.gz  | bgzip -c >mysample_gnomad.vcf.gz

Do you know what I missed?

Thanks a lot in advance,

All the best,

Laure

[Brent Pedersen]

Hi Laure, the output gets added to the INFO field, so you can see it with, e.g.:

zgrep -w gnmoAD_AF mysample_gnomad.vcf.gz

hope that helps. Otherwise, let me know if I've misunderstood.
-B

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[Laure Fresard]

Hi Brent,
Thanks for your answer.
The issue is that it does not get added to the INFO field, it is added to the header but nothing changed in the rest of the file.
Best,
Laure

[Laure Fresard]

I should maybe add that my INFO field in the vcf of origin is “.”
Best
Laure

[Brent Pedersen]

can you share an example line from your query vcf along with the header?

[Laure Fresard]

##fileformat=VCFv4.1

##fileDate=12-06-2017

##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">

##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">

##contig=<ID=1,length=249250621,assembly=GRCh37>

##contig=<ID=2,length=243199373,assembly=GRCh37>

##contig=<ID=3,length=198022430,assembly=GRCh37>

##contig=<ID=4,length=191154276,assembly=GRCh37>

##contig=<ID=5,length=180915260,assembly=GRCh37>

##contig=<ID=6,length=171115067,assembly=GRCh37>

##contig=<ID=7,length=159138663,assembly=GRCh37>

##contig=<ID=8,length=146364022,assembly=GRCh37>

##contig=<ID=9,length=141213431,assembly=GRCh37>

##contig=<ID=10,length=135534747,assembly=GRCh37>

##contig=<ID=11,length=135006516,assembly=GRCh37>

##contig=<ID=12,length=133851895,assembly=GRCh37>

##contig=<ID=13,length=115169878,assembly=GRCh37>

##contig=<ID=14,length=107349540,assembly=GRCh37>

##contig=<ID=15,length=102531392,assembly=GRCh37>

##contig=<ID=16,length=90354753,assembly=GRCh37>

##contig=<ID=17,length=81195210,assembly=GRCh37>

##contig=<ID=18,length=78077248,assembly=GRCh37>

##contig=<ID=19,length=59128983,assembly=GRCh37>

##contig=<ID=20,length=63025520,assembly=GRCh37>

##contig=<ID=21,length=48129895,assembly=GRCh37>

##contig=<ID=22,length=51304566,assembly=GRCh37>

##contig=<ID=X,length=155270560,assembly=GRCh37>

##contig=<ID=Y,length=59373566,assembly=GRCh37>

##contig=<ID=MT,length=16571,assembly=GRCh37>

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample

22 16123164 . C A . PASS . GT:VR:RR:DP:GQ 0/1:6:32:38:.

[Brent Pedersen]

So the problem is that vcfanno is expecting vcfs to have the suffix
".vcf.gz". You can get around this by doing

$ ln -s gnomad.genomes.r2.0.2.sites.chr22.vcf.bgz
gnomad.genomes.r2.0.2.sites.chr22.vcf.gz
$ ln -s gnomad.genomes.r2.0.2.sites.chr22.vcf.bgz.tbi
gnomad.genomes.r2.0.2.sites.chr22.vcf.gz.tbi

and then pointing the conf file to the symlink.

I have opened an issue to track this:
https://github.com/brentp/vcfanno/issues/81

thanks for reporting.
-Brent

[Laure Fresard]

Awesome, thanks a lot!
All the best,
Laure