How to make a vcf file using GWAS Catalog all_association.tsv file

Question

[Alexandros.Frydas]

Hello everyone,

I would like to ask if there is a way to generate a vcf file just by using the association_file you can download from the GWAS Catalog website ( https://www.ebi.ac.uk/gwas/docs/file-downloads_All associations v1.0.2 - with added ontology annotations, GWAS Catalog study accession numbers and genotyping technology).

I checked a previous related post (Convert association data from gwas catalog to vcf format) but using this script did not help, as I was not getting anything in the output file.

Thanks in advance!

Alex

Answer 1

[Pierre Lindenbaum]

but using this script did not help, as I was not getting anything in the output file.

works fine on my machine after updating the ftp->http

wget -q -O - "http://ftp.ebi.ac.uk/pub/databases/gwas/releases/2018/11/05/gwas-catalog-associations_ontology-annotated.tsv" | awk -F '\t' '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);}'

(...)
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   .   .   .   .
2   85567174    GCST001148  N   .   .   .   .
2   237478585   GCST001148  N   .   .   .   .
3   141383991   GCST001148  N   .   .   .   .
3   170412314   GCST001148  N   .   .   .   .
5   1279913 GCST001148  N   .   .   .   .
5   44365443    GCST001148  N   .   .   .   .
6   31150734    GCST001148  N   .   .   .   .
12  49282227    GCST001148  N   .   .   .   .
X   67801708    GCST001148  N   .   .   .   .

[Alexandros.Frydas]

Ok! Thanks a lot for the quick response!

Best, Alex

[Pierre Lindenbaum]

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