Question: A Non-Human Variants Data Analysis Error By Using Variants_Reduction.Pl
0
gravatar for Tonyzeng
6.3 years ago by
Tonyzeng300
Tonyzeng300 wrote:

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 • 1.7k views
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Tonyzeng300
1
gravatar for Neilfws
6.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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 COMMENTlink written 6.3 years ago by Neilfws48k

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.

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Tonyzeng300

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

ADD REPLYlink written 6.3 years ago by Tonyzeng300
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