Add dbSNP IDs to a VCF file that doesn't have them.

Add dbSNP IDs to a VCF file

#GATK Method <- Slower and keeps original ID plut dbSNP rsID
# R=Reference FASTA
# V=VCF file to add IDs to
# --dbsnp = dbsnp VCF -- download from NCBI FTP

java -jar GenomeAnalysisTK.jar -R /reference/Homo_sapiens_assembly19.fasta -T VariantAnnotator -V vcf_to_add_id_to.vcf --dbsnp /reference/dbsnp_137.b37.vcf.gz --out /data/Broad.chr1.annotated.vcf

#bcftools Method <- Faster, replaces existing ID with dbSNP rsID
/usr/bin/htslib/bcftools/bcftools annotate -a /reference/dbsnp_137.b37.vcf.gz -c ID vcf_to_add_id_to.vcf