Forked from obenshaindw/Add dbSNP IDs to a VCF file
Created
September 15, 2016 06:47
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Add dbSNP IDs to a VCF file that doesn't have them.
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#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 |
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