[ensembl-dev] VEP using CADD plugin
wm2 at ebi.ac.uk
Thu Jul 3 14:38:47 BST 2014
You should get the data file and index from the line:
All possible SNVs of GRCh37/hg19 [ file (79G)
| tabix index (2.7M)
On 3 July 2014 14:19, Eva Goncalves Serra <egs at sanger.ac.uk> wrote:
> I am a bit confused as to which file from
> http://cadd.gs.washington.edu/download I should download to use the
> plugin of CADD scores.
> Any help would be appreciated.
> From: Will McLaren <wm2 at ebi.ac.uk>
> Reply-To: Ensembl developers list <dev at ensembl.org>
> Date: Wednesday, 7 May 2014 16:13
> To: Ensembl developers list <dev at ensembl.org>
> Subject: Re: [ensembl-dev] VEP using CADD plugin
> Correct, the plugin was intended to work with the whole_genome_SNVs.tsv
> file, which only contains data for SNVs.
> I've modified the plugin so that it should be able to cope with indel
> data files such as you have; please do let me know if you have any problems
> as I've only sparingly tested it on made-up data!
> Will McLaren
> Ensembl Variation
> On 7 May 2014 15:37, Genomeo Dev <genomeodev at gmail.com> wrote:
>> There seem to be a discrepancy between the CADD score calculated using
>> VEP with the CADD.pm plugin and the tabix direct output:
>> For example using this 1000G variant:
>> #CHROM POSID REFALT QUALFILTER INFO
>> 7 86214932rs140931361 TTACTCT .PASS .
>> variant_effect_predictor.pl -i input.txt --format vcf --plugin
>> does not return any CADD score
>> $ tabix -p vcf 1000G.tsv.gz 7:86214932-86214932
>> 7 86214932TTACTC T-0.420243 2.040
>> This seems to affect indels and not SNVs. I could see in the plugin
>> that there is a rule to ignore indels. Any suggestions please how to safely
>> change that?
>> Also, in the plugin, I assume there is a test to ensure the alleles are
>> identical between the input file and the 1000G.tsv.gz file. Is this correct?
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