Question: Convert association data from gwas catalog to vcf format
0
gravatar for hsiaoyi0504
9 months ago by
hsiaoyi050440
Taiwan
hsiaoyi050440 wrote:

Hi there, I have a tsv file from GWAS-Catalog like this one in tsv format: ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2018/11/05/gwas-catalog-associations_ontology-annotated.tsv

However, for many annotation tools, they require input data as vcf format. Therefore, I would like to convert those SNPs into vcf format. Is there any tools I can use to directly do that ?

snp gwas-catalog gwas vcf • 380 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum122k • written 9 months ago by hsiaoyi050440
1
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

use awk to generate a header and create the VCF field. Here is a basic script.

 wget -q -O - "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2018/11/05/gwas-catalog-associations_ontology-annotated.tsv" | awk -F '     ' 'BEGIN{printf("##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n");}/^DATE ADDED/{next}{printf("%s\t%s\t%s\tN\t.\t.\t.\t.\n",$12,$13,$37);}'

##fileformat=VCFv4.2
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
6   32251212    GCST001156  N   .   .   .   .
6   32441753    GCST001156  N   .   .   .   .
6   33075103    GCST001156  N   .   .   .   .
6   32623148    GCST001156  N   .   .   .   .
6   31039078    GCST001181  N   .   .   .   .
6   31125810    GCST001181  N   .   .   .   .
6   31168676    GCST001181  N   .   .   .   .
6   31440051    GCST001181  N   .   .   .   .
ADD COMMENTlink written 9 months ago by Pierre Lindenbaum122k
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