A Non-Human Variants Data Analysis Error By Using Variants_Reduction.Pl
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8.6 years ago
Tonyzeng ▴ 310

When I run variants_reduction script of Annovar for the mouse variant file, it shows as follows, but this script should support for non-human variants according to the manual, Any suggestions? thank you!

  $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'  annovar • 2.2k views ADD COMMENT 1 Entering edit mode 8.6 years ago Neilfws 49k It's not clear from the manual whether variants_reduction.pl is supposed to work for non-human variants. The syntax is similar to annotate_variation.pl but non-human examples are not given. I have not looked at the code (since it requires registration) but presumably, it uses something like Getopt to check the command-line parameters. So if it says "must be hg18 or hg19" - well, that is what it means. I would contact the authors for clarification (then post their reply here as an answer, to help others). ADD COMMENT 0 Entering edit mode Hi, Neilfws, I've contacted with author for clarification and he suggested me to use table_annovar.pl instead of using reduction.pl. But please go ahead to contact with author since table_annovar can only produce a table that can be opend in excel but I do need to filter variants from sanger mouse dbsnp data and then I will generate a excel spreadsheet. also when I run table_annovar.pl $ table_annovar.pl -buildver mm10 snps.annovar.exonic_variant_function mm10db/ -protocol nonsyn_splicing,genomicSuperDups,SC_MOUSE_GENOMES.genotype.vcf,dominant -operation g,rr,f,m -nastring NA


It did not work because SC_MOUSE_GENOMES.genotype.vcf ( downloaded from Sanger) is not a default data under mm10. I do need to figure this out but it is a little complex now.

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I forget to mention that mm10db is the data package that i downloaded exactly according to the ANNOVAR manual. there is no variants or dbsnp data in this package. so I have to download variant data (SC_MOUSE_GENOMES.genotype.vcf), but it did not work for table_annovar.pl at all