A Non-Human Variants Data Analysis Error By Using Variants_Reduction.Pl

Question

[Tonyzeng]

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'

Answer 1

[Neilfws]

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).

[Tonyzeng]

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.

[Tonyzeng]

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