Entering edit mode
2.7 years ago
robjohn70000
▴
160
Hi,
I have a vcf file with the following fields:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleX
The issue is that the ID column has '.' and no rsids. I have an annotation file in gtf format as follows:
1 AUGUSTUS CDS 106955274 106955412 0.89 + 0 transcript_id "g53770.t1"; gene_id "g53770";
1 AUGUSTUS intron 106955413 107007218 0.89 + . transcript_id "g53770.t1"; gene_id "g53770";
Does anyone know how I can use the annotation file to add rsids to my vcf file?
Thanks
Thanks @Pierre Lindenbaum Any idea how I can obtain the dbsnp-like vcf?
Download it from dbSnp
https://www.ncbi.nlm.nih.gov/snp/
Problem solved. Thanks @Pierre Lindenbaum and @Istvan Albert