Which database can be used to identify canonical splice site altering for ANNOVAR?
0
0
Entering edit mode
2.3 years ago
Shicheng Guo ★ 8.8k

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 • 638 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1886 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6