Locus in my snps.vcf file

Question

[abrahamthz]

Hello sorry to trouble you, but I am working with Arabidopsis and In my final file result using GATK I have this information from snps in my sample:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  PA01                                                            
1   32210   0   T   C   13.22   LowQual AC=1    AF=1.00 AN=1    BaseQRankSum=-0.389 ClippingRankSum=0.000   DP=11   FS=7.404    MLEAC=1 MLEAF=1.00  MQ=60.00    MQRankSum=0.000 QD=1.20 ReadPosRankSum=-0.275   SOR=3.352   GT:AD:DP:GQ:PL  1:5 6:11:43:43  0

Do you know how I can get the information of gene description or localization from those snps? (For example AT5G28540)

Thanks in advance

Abraham

[iraun]

Have you tried to annotate your snps using a tool like SnpEff? It annotates and predicts the effects of variants on genes (and of course, you will get the gene name).

Answer 1

[Matthieu Miossec]

Submit your VCF file to ANNOVAR, it will provide all the annotation you need:

http://wannovar.usc.edu/

[harold.smith.tarheel]

WebAnnovar is limited to human data and therefore unsuitable for the OP's Arabidopsis sample.

[ivivek_ngs]

Ah yes that is also another thing. In that case VEP will be a better resource or command line annovar which comes with a bundle for species if I reckon correctly

[Matthieu Miossec]

That is true, my mistake.

[ivivek_ngs]

webannovar has a restriction to the number of variants that it takes as input in a sinlge vcf file as far as I remember, so it depends on the total number of variants in the file of OP, if its less than 500 then web annovar is fine else use the command line , or VEP or SNPeff as suggested by @iarun