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
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abrahamthz •
Submit your VCF file to ANNOVAR, it will provide all the annotation you need:
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
WebAnnovar is limited to human data and therefore unsuitable for the OP's Arabidopsis sample.
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
That is true, my mistake.
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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).