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Old 05-28-2012, 05:07 AM   #1
rechu
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Question Annovar

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...
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Old 05-28-2012, 06:32 AM   #2
Heisman
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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.
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Old 05-28-2012, 10:38 PM   #3
rechu
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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?
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Old 05-29-2012, 06:27 AM   #4
Heisman
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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?
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Old 05-30-2012, 01:40 AM   #5
rechu
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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!!!
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