Question: Hello every one, can any one suggested a tool or method to get rsID for a number variants I have in vcf file, do I have to manipulate the header for my file? Many thanks for your help in advance

The vcf file I have in this shape:

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##fileformat=VCFv4.1
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##LeftAlignVariants="analysis_type=LeftAlignVariants bypassFlowAlign=true kmer_len=19 min_var_count=5 short_suffix_match=5 min_indel_size=4 max_hp_length=8 min_var_freq=0.15 min_var_score=10.0 relative_strand_bias=0.8 output_mnv=0 sse_hp_size=0 sse_report_file= target_size=1.0 pref_kmer_max=3 pref_kmer_min=0 pref_delta_max=2 pref_delta_min=0 suff_kmer_max=3 suff_kmer_min=0 suff_delta_max=2 suff_delta_min=0 motif_min_ppv=0.2 generate_flow_position=0 input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/results/referenceLibrary/tmap-f3/hg19/hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 combined_sample_name= num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/results/analysis/output/Home/MGHBED_602/plugin_out/variantCaller_out/IonXpress_001/small_variants.sorted.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filter_mismatching_base_and_quals=false"
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##fileDate=20140616
##phasing=none
##reference=/results/referenceLibrary/tmap-f3/hg19/hg19.fasta
##reference=file:///results/referenceLibrary/tmap-f3/hg19/hg19.fasta
##source=Torrent Unified Variant Caller (Extension of freeBayes)
#CHROM POS ID REF ALT QUAL FILTER
chr1 65886142 . C G 97.35 PASS
```

Answer: For VCF annotation with rsids, you may need dbSNP VCF file (hg19=b37.x build based dbSNP VCF) in addition to sample(s) vcf. You need to index VCF files and then use tools suggested: GATK variant annotator (mentioned above by Pierre Lindenbaum), Snpsift, bcftools Note that dbSNP vcf (for entire b37) is huge. You can also use web based annotation tool (http://www.ncbi.nlm.nih.gov/variation/tools/reporter/) from NCBI.

**Example code for bcftools**:

bcftools annotate -c ID -a dbsnp.vcf.gz sample1.vcf.gz > sample1.rs.vcf

**Example code for snpsift**:

java -jar SnpSift.jar annotate dbsnp.vcf sample1.vcf > sample1.rs.vcf