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 ?
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	.	.	.	.

