Hello, I am trying to use vcfanno tool to annotate my query VCF file with the CADD v1.6 files that I have installed. These files come as "tsv.gz" files with the following format which resembles neither VCF (where I would use the "fields=" option) nor BED (where I would use the "columns=" option):
## CADD GRCh38-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved.
#Chrom Pos Ref Alt RawScore PHRED
1 10001 T A 0.702541 8.478
1 10001 T C 0.750954 8.921
1 10001 T G 0.719549 8.634
1 10002 A C 0.713993 8.583
1 10002 A G 0.743661 8.854
I have tried both vcfanno options. With "fields=" in the config file, it runs but nothing is annotated. With "columns=" it generates the following error: "panic: toml: cannot load TOML value of type string into a Go integer"
thanks for your help.
1 answer
Came across this very relevant link: http://brentp.github.io/vcfanno/examples/cadd/
I followed the instruction and it runs with the following output
vcfanno version 0.3.2 [built with go1.12.1]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 4 sources from 2 files
vcfanno.go:145: using 2 worker threads to decompress bgzip file
vcfanno.go:248: annotated 4758 variants in 2.08 seconds (2288.1 / second)
the "RawScore" and "Phread" lines are added to my VCF header but none of the variants are annotated with these fields.
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