SNP ID

Question

[shamsurrahaman132]

Hello Community,

I'm Shamsur. I was dealing with variant calling.

Is it possible to get snp id's while generating vcf file, like this image

I got this from my professor. It represent bangladeshi goat breed snp. Here this vcf file has ID for snp's and also dbSNP_143 was used to get these ID's.

Now here is what I got while doing varient calling. In my case ID has a dot(.). I did not get any ID for this vcf file. Someone please help me, how can I get vcf file with ID's

Thank you.

[brunobsouzaa]

If I'm not wrong, in GATK, you can pass the -D argument in HaplotypeCaller and pass your DBSNP file as input. But, you can always annotate your vcf file after generating it!

[shamsurrahaman132]

Thank you. @brunobsouzaa.

I did look at GATK documentation and your suggation worked.

Answer 1

[Emily]

Most variant callers don't look up variant ID. You would need to run your VCF through a variant annotator, eg VEP to add ID and other useful annotation.

[shamsurrahaman132]

Thank you @Emily_Ensembl

This one is new for me. I will check it out.