[ensembl-dev] variation database usage

Thu Feb 16 11:30:16 GMT 2012

Hi Will

Thank you for your quick response. I tried to run the following command and it failed with a  message.

2012-02-16 22:13:34 - Starting...
2012-02-16 22:13:36 - Read 54138 variants into buffer
2012-02-16 22:14:40 - Checking for existing variations
[==================================================================================================================================]  [ 100% ]
2012-02-16 22:14:56 - Analyzing chromosome 22
2012-02-16 22:14:57 - Reading transcript data from cache and/or database
[==================================================================================================================================]  [ 100% ]
2012-02-16 22:16:29 - Retrieved 4466 transcripts (0 mem, 0 cached, 8575 DB, 4109 duplicates)
2012-02-16 22:16:29 - Analyzing variants
[==================================================================================================================================]  [ 100% ]
2012-02-16 22:18:07 - Reading regulatory data from cache and/or database
[==================================================================================================================================]  [ 100% ]
2012-02-16 22:18:54 - Retrieved 19317 regulatory features (0 mem, 0 cached, 22312 DB, 2995 duplicates)
2012-02-16 22:18:54 - Analyzing RegulatoryFeatures
[==================================================================================================================================]  [ 100% ]
2012-02-16 22:18:55 - Analyzing MotifFeatures
[==================================================================================================================================]  [ 100% ]
2012-02-16 22:19:01 - Calculating and writing output
[>                                                                                                                                 ]    [ 0% ]
Can't call method "get_all_Alleles" on an undefined value at /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 3400, <GEN0> line 54165.

COMMAND:

perl5.14.2 variant_effect_predictor.pl --output_file chr22.vep --species homo_sapiens --host cg.anu.edu.au --user compgen --password compgen --port 3306 --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical --hgnc --regulatory --protein --gene --condel b --polyphen b --sift b --force_overwrite --input_file chr22.1000.vcf --check_existing --check_frequency --check_alleles --freq_pop any --per_gene --freq_freq 0 --freq_filter include --freq_gt_lt gt

Could you please let me know what am I doing wrong?

Kind regards

Hardip R. Patel, PhD
Post-doctoral Research Fellow

Genome Discovery Unit and RNA Biology Lab
Genome Biology Department
The John Curtin School of Medical Research
College of Medicine, Biology and Environment
The Australian National University
Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
Phone Number: (+61) 0449 180 715

On 16/02/2012, at 9:45 PM, Will McLaren wrote:

> Hi Hardip,
> 
> You may find it easier to use the VEP for this as it wraps up a lot of
> the functionality you are interested in already. You could get it to
> check for phenotypes by creating a bed file or similar of
> phenotype-associated loci, tabix indexing it and using it as a custom
> data source for the VEP (see
> http://www.ensembl.org/info/docs/variation/vep/vep_script.html#custom).
> 
> The VEP can also compare to existing variations, and their alleles,
> using --check_existing and --check_alleles.
> 
> If you do want to continue with the API, here's some code that should
> get you started - I'm assuming you have your VF object created in
> $new_vf, and that you are connected to the database already.
> 
> Cheers
> 
> Will McLaren
> Ensembl Variation
> 
> # attach a slice to the VF, it probably doesn't have one
> my $sa = $reg->get_adaptor("human","core","slice");
> my $slice = $sa->fetch_by_region("chromosome", $new_vf->{chr});
> $new_vf->{slice} = $slice;
> 
> # get overlapping existing VFs from the variation database by fetching
> from the feature slice of the new VF
> foreach my $existing_vf(@{$new_vf->feature_Slice->get_all_VariationFeatures}) {
> 
>  # compare alleles
>  print "New alleles!\n" if $new_vf->allele_string ne
> $existing_vf->allele_string;
> 
>  # get phenotype annotations via the variation object
>  foreach my $va(@{$existing_vf->variation->get_all_VariationAnnotations}) {
>     print $existing_vf->variation_name, " is associated with
> phenotype ", $va->phenotype_description, "\n";
>  }
> }
> 
> On 16 February 2012 10:21, Hardip Patel <hardip.patel at anu.edu.au> wrote:
>> Dear all
>> 
>> I have vcf files generated for individual chromosomes from a human
>> resequencing project. I was wondering if somebody could get me started with
>> ways to use the variation api.
>> 
>> I am mainly interested in knowing following from my vcf files.
>> 
>> Is the variation in vcf is found in dbSNP and if yes, is it the same
>> genotype as the one in my vcf file?
>> Is the variation implicated in NHGRI_GWAS catalogue or not?
>> 
>> I have tried reading documentation on variation api and i am not able to
>> come up with a way to do this.
>> 
>> I am able to use parse_vcf subroutine to parse vcf line and get a variation
>> feature object. I am getting stuck after that in that I am not sure how to
>> use the variationfeature to ask the above questions.
>> 
>> Any help is greatly appreciated.
>> 
>> 
>> Kind regards
>> 
>> 
>> Hardip R. Patel, PhD
>> Post-doctoral Research Fellow
>> 
>> Genome Discovery Unit and RNA Biology Lab
>> Genome Biology Department
>> The John Curtin School of Medical Research
>> College of Medicine, Biology and Environment
>> The Australian National University
>> Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
>> Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
>> Phone Number: (+61) 0449 180 715
>> 
>> 
>> 
>> 
>> 
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> 
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