Question: Using vcfanno to annotate VCF file with CADD1.6 "tsv.gz" files
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gravatar for NGSCanBioinf
4 days ago by
NGSCanBioinf10
Canada
NGSCanBioinf10 wrote:

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.

vcfanno annotation • 79 views
ADD COMMENTlink modified 3 days ago • written 4 days ago by NGSCanBioinf10
1

Tagging brentp

ADD REPLYlink written 4 days ago by RamRS30k
0
gravatar for NGSCanBioinf
3 days ago by
NGSCanBioinf10
Canada
NGSCanBioinf10 wrote:

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.

ADD COMMENTlink written 3 days ago by NGSCanBioinf10
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