This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Which database can be used to identify canonical splice site altering for ANNOVAR?

Hi All,

Which database can be used for ANNOVAR to identify canonical splice site altering? I find ANNOVAR can identify stop-gain and stop-lost very easily. However, I didn't find any database for ANNOVAR to identify canonical splice site altering.

Thanks. 

table_annovar.pl ./annovar/gnomad.exomes.r2.1.sites.chr22.rec.vcf.avinput ~/annovar/humandb/ --thread 4 -buildver hg19 --csvout -out ./annovar/chr22 -remove -protocol refGene,dbnsfp33a,gwasCatalog,wgRna,targetScanS,tfbsConsSites -operation gx,f,r,r,r,r -nastring . -otherinfo -polish -xref ~/humandb/gene_fullxref.txt
annovar splice site
• 1,578 views • link
updated by lincaijin1994 • lincaijin1994 • written by Shicheng Guo Shicheng Guo

Hi, I have the same question. Have you found the solution? In some papers, they defined the canonical splice variants as those +/- 1 or 2. Also, some literatures stated that splice_site variants in the penultimate or the last exons were excluded. I dont know how to identify splice_site variants in the penultimate or the last exons.

• 0 views • link
written by lincaijin1994 • lincaijin1994

0 answers

No answers yet.

Log in to answer this question.

More posts like this