This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extracting specific SNPs from VCF

Hi,

How should I extract specific SNPs from VCF file (30x). What is the standard way of doing this? Which tool/s should I use?

I have file with the snp ids (ie. rs964284,...) I would like to extract and the 30x vcf which is not annotated.

Right now I would imputate the vcf (beagle), annotate it (variant annotator) and then extract the SNPs.

Is there a tool that does it all in one go?

Thanks.

vcf gatk snp
• 1,838 views • link
updated by Kevin Blighe Kevin Blighe • written by igor • igor

1 answer

Is there a tool that does it all in one go?

Not really, but you can develop one now, if you want? If anything comes close, then it's the GATK due to the fact that it has a BeagleCodec, but you would still need to run Beagle first.

For imputation, there is also IMPUTE2 or SHAPEIT2+IMPUTE2. For annotation, you can use bcftools, SnpEff, or, indeed, GATK's VariantAnnotator. For extracting the SNPs, use bcftools filter, bcftools view, GATK, or just your own shell scripts (awk works well), or even Python.

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

Kevin thanks for the reply. I could write such app. How should I think about imputation and coverage? Should I do imputation on 30x vcf, or whatever is not in 30x vcf equals the reference? Thanks.

• 0 views • link
written by igor • igor

Log in to answer this question.

More posts like this