Annovar

[rechu]

hey hello,
i have one question that should ANNOVAR is used only for SNP detection in Human? isn,t it work on other species please give me some guideline i really don't
know...

[Heisman]

The databases that come with ANNOVAR are only for human (hg18 or hg19 reference sequences). You can use ANNOVAR to easily query any database if you can create/download relevant databases for other organisms.

[rechu]

Means using another organisms database we can use ANNOVAR for snp detection right..but then what we have to do if we don't have another organisms database????

i explain i want to find SNPs in buffalo genome for that i want to use ANNOVAR so what i have to do exactly? because for buffalo i have filtered read and quality files for that....by using this cant i use ANNOVAR?

[Heisman]

Oh, I see. ANNOVAR is NOT a SNP caller; it is used to annotate SNPs you can look into using the GATK or SAMtools if you want to simply get a list of SNPs for your organism (assuming there is a known reference sequence for the organism in question). Is there a buffalo reference sequence available?

[rechu]

ok ok thanks you for answering, my organism for project is buffalo and its reference is Bos taurus, and information related to bos taurus is available. thank u again for answering.. if i have any query related to ANNOVAR i will ask!!!