This is a small script can help to annotate your SNPs. The program take on input your SNP-ID from the VCF file and generate a report based on SNPedia (https://www.snpedia.com/) data.
Firstly, you need to convert the file for reading. To do this, filter out the unique SNP-IDs by bash:
Note: If you want to select clinically relevant SNPs, you can use the Clinwar database - download a VCF with ClinVar variants (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz). You should also download SnpSift (https://pcingola.github.io/SnpEff/)
java -jar SnpSift.jar annotate clinvar.vcf snps.vcf > snps_snpsift_clinvar.vcf # Filtering out the necessary columns in the original vcf file
egrep -v '^#|^$' snps_snpsift_clinvar.vcf | cut -f 1-6,10 > snp_python.txt
# Select the identifiers of SNPs
awk '($32!="-")' snps_snpsift_clinvar.txt | grep risk_factor | cut -f 1-3,19 | sort | uniq > sorted_SNP.txt
cut -f 3 sorted_SNP.txt | uniq > zzz.txt
cut -d ';' -f1 zzz.txt > SNP_identificators.txtUse SNParser.py script and enjoy.
Note: The input script accepts two files: SNP_identificators.txt and you 'raw' VCF snp_python.txt in TXT format!
As a result you should to get html file, which will contain something like that:
