error while annotating vcf file using snpEff
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6 months ago
rheab1230 ▴ 50

I want to annotate my vcf file with geneid of Ensembl. I used snpEff tool to annotate vcf file with geneID of Ensembl. But in my case its the same gene ID being assigned for every rsid. This is the command I used for running the tool:

java -jar snpEff.jar -v GRCh37.75 chr22_annotate.vcf > chr22_ann_geneid1.vcf

This is the output:

22 16050213 rs587654921 C T 100.0 PASS AC=38;AF=0.00758786;AN=5008;NS=2504;DP=15092;EAS_AF=0;AMR_AF=0.0014;AFR_AF=0.0272;EUR_AF=0.001;SAS_AF=0;AA=.|||;VT=SNP;ANN=T|intergenic_region|MODIFIER|CHR_START-LA16c-4G1.3|CHR_START-ENSG00000233866|intergenic_region|CHR_START-ENSG00000233866|||n.16050213C>T||||||

22 16050319 rs587712275 C T 100.0 PASS AC=1;AF=0.000199681;AN=5008;NS=2504;DP=22609;EAS_AF=0;AMR_AF=0.0014;AFR_AF=0;EUR_AF=0

;SAS_AF=0;AA=.|||;VT=SNP;ANN=T|intergenic_region|MODIFIER|CHR_START-LA16c-4G1.3|CHR_START-ENSG00000233866|intergenic_region|CHR_START-ENSG00000233866|||n.160

50319C>T||||||

22 16050527 rs587769434 C A 100.0 PASS AC=1;AF=0.000199681;AN=5008;NS=2504;DP=23591;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;AA=.|||;VT=SNP;ANN=A|intergenic_region|MODIFIER|CHR_START-LA16c-4G1.3|CHR_START-ENSG00000233866|intergenic_region|CHR_START-ENSG00000233866|||n.16050527C>A|

geneid annotation snpEff ensembl • 437 views
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6 months ago

I think this is correct - those snps are all upstream of ENSG00000233866

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Thank you.

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