updating SNP names in VCF file

Question

[mel22]

Hello How can I update SNP names from position (chr1:xxxxxx) to rs name in VCF file ? I have a reference VCF file with rs names and want to update my own data VCF file.

Thanks for your help

[cpad0112]

intersect sample vcf with reference vcf with bedtools or annotate with bcftools

Answer 1

[Arup Ghosh]

dbSNP annotation can be added in the ID filed using the VariantAnnotator tool from GATK.

gatk  --java-options '-Xmx4G' \
   VariantAnnotator \
   -R /userdata/arup/hpcc_test/genome/hg38/hg38.fa \
   -V input.vcf.gz \
   -O output.vcf.gz \
   --dbsnp dbsnp.vcf.gz

[mel22]

Thank you very much

Answer 2

[Jimbou]

you can also use SnpSift from the SnpEff package http://snpeff.sourceforge.net/SnpSift.html#annotate

 java -jar SnpSift.jar annotate dbSnp132.vcf input.vcf > output_annotated.vcf

check ftp://ftp.ncbi.nih.gov/snp/organisms/ for other dbSNP builds

[mel22]

Thank you very much