Question: Help understanding CHROM and POS fields in VCF
0
gravatar for bdolin
4 weeks ago by
bdolin90
Elimu Informatics
bdolin90 wrote:

Greetings,

Can someone explain how to relate CHROM and POS in VCF to the corresponding position in the referenced dbSNP?

For instance, in the following example:

#CHROM POS     ID        REF ALT
20     14370   rs6054257 G      A

It looks as though the VCF is referring to a variant on Chr20 at position 14370, but the referenced dbSNP has HGVS NC_000020.10:g.66370G>A.

If the VCF record didn't include the dbSNP id, how would one convert this into an HGVS expression?

Thanks

sequence genome • 159 views
ADD COMMENTlink modified 4 weeks ago by finswimmer730 • written 4 weeks ago by bdolin90
1
gravatar for WouterDeCoster
4 weeks ago by
Belgium
WouterDeCoster26k wrote:

Your interpretation about chrom and pos is correct. Keep in mind that this is the chromosome coordinate, and that HGVS is based on genes/transcripts. For annotation you can use VEP or Snpeff, which will give you HGVS notation.

ADD COMMENTlink written 4 weeks ago by WouterDeCoster26k

Thank you for your answer. If VCF Pos=14370, how can it be that corresponding HGVS has position 66370?

ADD REPLYlink written 4 weeks ago by bdolin90
0
gravatar for finswimmer
4 weeks ago by
finswimmer730
Germany
finswimmer730 wrote:

Hello,

which reference sequence did you use for alignment and variant calling? I guess something went wrong here. Because rs6054257 is located on chromosome 20 at position 66370 if you use hg19 or at position 85729G for hg38.

At position 14370 are no variants known as this region could not be sequenced successfully until now. There are just Ns.

fin swimmer

ADD COMMENTlink written 4 weeks ago by finswimmer730

Here is where I took the example from: http://www.internationalgenome.org/wiki/Analysis/vcf4.0/

ADD REPLYlink written 4 weeks ago by bdolin90

I believe that's hg18.

ADD REPLYlink written 4 weeks ago by WouterDeCoster26k

That was my thought either after sending my answer. In the linked example there is a header

##reference=1000GenomesPilot-NCBI36

which is hg18.

fin swimmer

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by finswimmer730
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