ANNOTATE Homo_sapiens.gene_info.gz in vcf file?

Question

[cristina_sabiers]

Hi!

Which tools I can use to annotate for example the Homo_sapiens.gene_info.gz on my vcf file? I asume I must focus on Symbol (gene) to annoate the rest of values, I tried few things but no lucky :(

Thanks!!!

[Pierre Lindenbaum]

how about 'just' using VEP or SNPEFF to get the gene name?

[GenoMax]

Use information from Homo_sapiens.gene_info.gz to annotate your vcf file? Anything special about this file? Is snpEff not acceptable?

[cristina_sabiers]

I dont know how to answer both at same time, so I post it here, hope its ok.

well I must say I just know how to annotate clinvar and gen.bed file, I tried this

java -Xmx1g -jar /media/cri/CRIS_DATA/SNEPF/snpEff/SnpSift.jar \
annotate \
-v \
Homo_sapiensgene_info.vcf \
test.vcf \
> testout.vcf

I m not just interested on the gene, more like in Nomenclature_status Other_designations....

 #tax_id    GeneID  Symbol  LocusTag    Synonyms    dbXrefs chromosome  map_location    description type_of_gene    Symbol_from_nomenclature_authority  Full_name_from_nomenclature_authority   Nomenclature_status Other_designations  Modification_date
9606    1   A1BG    -   A1B|ABG|GAB|HYST2477    MIM:138670|HGNC:HGNC:5|Ensembl:ENSG00000121410|Vega:OTTHUMG00000183507  19  19q13.43    alpha-1-B glycoprotein  protein-coding  A1BG    alpha-1-B glycoprotein  O   alpha-1B-glycoprotein|HEL-S-163pA|epididymis secretory sperm binding protein Li 163pA   20161206