How to add rsIDs to VCF?

Question

[markgodek]

I'm still a beginner and using Illumina Platinum Genomes as a toy dataset. Google supplies the files in VCF, but I need them annotated with rsIDs.

I've tried GATK VariantAnnotator and bcftools annotate as suggested by this post I found via Google and this Biostars post, but I'm not having any luck.

When the command line finishes running, the output doesn't have the rsIDs filled in and no obvious errors pop up. I'm kinda stumped.

Any help is appreciated.

[Pierre Lindenbaum]

I've tried GATK VariantAnnotator and bcftools annotate as suggested by this post I found via Google, but I'm not having any luck.

show us your command lines.

[markgodek]

gatk VariantAnnotator -R '/home/mark/Desktop/Reference_Genome_hg19/hg19.fa' -I '/home/mark/Desktop/Google_CEPH_Genomes_hg19/platinum-genomes_bam_NA12877_S1.bam' -V '/home/mark/Desktop/CEPH VCFs/platinum-genomes_vcf_NA12877_S1.genome.vcf.gz' -O '/home/mark/Desktop/CEPH VCFs/GATK_NA12877_S1_rsids.genome.vcf' -L '/home/mark/Desktop/CEPH VCFs/platinum-genomes_vcf_NA12877_S1.genome.vcf.gz' --dbsnp '/home/mark/Desktop/Google_CEPH_Genomes_hg19/common_all_20180418.vcf.gz' 


bcftools annotate -a '/home/mark/dbsnp_138.b37.vcf.gz' -c ID '/home/mark/Desktop/CEPH VCFs/platinum-genomes_vcf_NA12877_S1.genome.vcf.gz' -o '/home/mark/Desktop/CEPH VCFs/NA12877_with_rsIDs.vcf.gz'

[nanodano]

I'm doing this but am struggling to get bcftools to work for some reason. It keeps annotating positions where ID should be in the VCF, and when I try and run with only -c ID, I get the following error: The -c CHROM option not given

Answer 1

[erkinacar5]

Hey it's quite some time ago but if anyone else is having a problem I just wanted to say following command worked for me:

bcftools annotate -a /data/references/hg19/pipe/dbsnp138/00-All.vcf.gz -c ID -o samtools_annotated.vcf.gz samtools.vcf.gz

The thing to look out for is, I think it doesn't work if your reference has numeric chromosome column while your VCF file has it as with 'chr' added to is, e.g. "chr1".

[markgodek]

Thanks for the follow up. I'm working on a different project now but I was able to add the rsIDs with bcftools.

I think the issue before was I was expecting more locations to have an rsID, but the NA12877 genome is so large there are just so many positions that aren't variants so it was hard to tell if it worked.

[Nai]

I want to add SNP ID and chromosomal Position in SNP_Matrix.txt or VCF file by replacing "."