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12-06-2011, 09:54 AM
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#1 |
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Member
Location: Germany Join Date: Mar 2011
Posts: 68
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annovar mouse
Hi everyone,
I use annovar for SNP annotation in human and would like to use the summarize_annovar.pl script for mouse as well. Unfortunally the script does just accept hg18 and hg19 as input for the parameter buildver. Is there any possibility to use that script for annotation? Thanks Robby |
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12-06-2011, 10:37 AM
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#2 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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I use it for mouse all the time. But you do have to download the mouse genome, and use buildver mm9.
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10-14-2013, 09:59 PM
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#3 |
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Member
Location: australia Join Date: Apr 2013
Posts: 15
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Can someone please tell me how to achieve this? I use --buildver mm9 and I get this error:
Error in argument: the --buildver argument must be 'hg18' or 'hg19' |
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11-04-2013, 12:28 PM
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#4 | |
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Member
Location: houston Join Date: Aug 2013
Posts: 19
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Hi, I may have the same problem as yours
I use [$ variants_reduction.pl snps.annovar mm10db/ -protocol nonsyn_splicing,genomicSuperDups,SC_MOUSE_GENOMES.genotype.vcf,dominant -operation g,rr,f,m -out reduce -buildver mm10 & Error in argument: the --buildver argument must be 'hg18' or 'hg19'] [/CODE] Quote:
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