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Description
According to https://github.com/brentp/vcfanno#typecasting-values, it should be possible to typecast fields by adding a _float suffix to the field names. However, when using the by_alt op, the annotated VCF fields do not have the desired type, and the _float suffixes are not removed
Op: self
Field name: good
Field number: bad
Field type: float
root@b3cca58b784e:/tmp# cat conf.toml
[[annotation]]
names = [ "CADD_RAW_float",]
file = "/tmp/annotation.tsv.gz"
columns = [ 5,]
ops = [ "self",]
root@b3cca58b784e:/tmp# vcfanno conf.toml test.vcf.gz
=============================================
vcfanno version 0.3.1 [built with go1.11]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 1 sources from 1 files
vcfanno.go:143: using 2 worker threads to decompress query file
api.go:804: WARNING: using op 'self' when with Number='1' for '' from '/tmp/annotation.tsv.gz' 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.
##fileformat=VCFv4.2
##contig=<ID=chr2,length=242193529,assembly=GRCh38>
##INFO=<ID=AF,Number=.,Type=Float,Description="">
##INFO=<ID=AQ,Number=.,Type=Integer,Description="">
##INFO=<ID=CADD_RAW,Number=1,Type=Float,Description="calculated by self of overlapping values in column 5 from /tmp/annotation.tsv.gz">
##hailversion=0.2.9-8588a25687af
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr2 41647 2_41647_A_G A G 1328.0 . AF=1.56250e-02;AQ=1328;CADD_RAW=0.591814
vcfanno.go:241: annotated 1 variants in 0.00 seconds (2292.6 / second)
Op: by_alt
Field name: bad
Field number: good
Field type: string
root@b3cca58b784e:/tmp# cat conf.toml
[[annotation]]
names = [ "CADD_RAW_float",]
file = "/tmp/annotation.tsv.gz"
columns = [ 5,]
ops = [ "by_alt",]
root@b3cca58b784e:/tmp# vcfanno conf.toml test.vcf.gz
=============================================
vcfanno version 0.3.1 [built with go1.11]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 1 sources from 1 files
vcfanno.go:143: using 2 worker threads to decompress query file
##fileformat=VCFv4.2
##contig=<ID=chr2,length=242193529,assembly=GRCh38>
##INFO=<ID=AF,Number=.,Type=Float,Description="">
##INFO=<ID=AQ,Number=.,Type=Integer,Description="">
##INFO=<ID=CADD_RAW_float,Number=A,Type=String,Description="calculated by by_alt of overlapping values in column 5 from /tmp/annotation.tsv.gz">
##hailversion=0.2.9-8588a25687af
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr2 41647 2_41647_A_G A G 1328.0 . AF=1.56250e-02;AQ=1328;CADD_RAW_float=0.591814
vcfanno.go:241: annotated 1 variants in 0.00 seconds (3546.0 / second)
It would be good if the following was true:
- Op:
by_alt - Field name: CADD_RAW
- Field number: A
- Field type: float
-
minimal conf and lua files that you are using.
See above -
urls or actual files for annotations in conf file.
root@b3cca58b784e:/tmp# zcat annotation.tsv.gz
## CADD GRCh38-v1.4 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2018. All rights reserved.
#Chrom Pos Ref Alt RawScore PHRED
2 41647 A G 0.591814 8.493
- minimal query file.
root@b3cca58b784e:/tmp# zcat test.vcf.gz
##fileformat=VCFv4.2
##contig=<ID=chr2,length=242193529,assembly=GRCh38>
##INFO=<ID=AF,Number=.,Type=Float,Description="">
##INFO=<ID=AQ,Number=.,Type=Integer,Description="">
##hailversion=0.2.9-8588a25687af
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr2 41647 2_41647_A_G A G 1328.0 . AF=1.56250e-02;AQ=1328
-
the command you used to invoke vcfanno
See above -
the full error message
None
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