Question: whole genome annotation using annovar, what is -xref example/gene_xref.txt?
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gravatar for Sharon
10 months ago by
Sharon420
Sharon420 wrote:

Hi Everyone

For annotating whole genome tsv files with annovar, I converted my whole genome var.tsv file to annovar input format using:

${ANNOVAR}/convert2annovar.pl -format cg -out fxxm1.annovar.input  var-GS00x-ASM.tsv

To annotate I used:

${ANNOVAR}/table_annovar.pl fxxm1.annovar.input  ${ANNOVAR}/humandb/ -buildver hg19 -out ${M1} -remove -protocol refGene,ensGene,cytoBand,gnomad_exome,exac03,avsnp147,\
        dbnsfp30a,clinvar_20170130,mitimpact2,revel -operation g,g,f,f,f,f,f,f,f,f  -nastring . -csvout -polish -xref ${ANNOVAR}/example/gene_xref.txt

My question is about: example/gene_xref.txt

Should I use the same file in annovar example folder or I should generate my own file gene_xref.txt? If yes, how this annotation file is generated.

Thanks

whole genome annovar • 381 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by Sharon420
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