[ensembl-dev] Variation (VEP) - Het/Hom Output

[Ricardo Parolin Schnekenberg]

Hi Will,

Sorry for not being so clear.
I am talking about the Perl script (2.5). Here at the centre we call our
variants with Platypus which outputs a nice VCF file in which the last
column tells us the genotype for each variant ([0/0] 0/1 1/0 1/1). Due to
some bugs in Annovar (which used this genotype column very well and output
HET or HOM based on that) we decided to try using VEP for our project. It
would be useful if VEP could do the same thing. Currently I had to write a
script that reads the output of VEP, grabs the location of the variant,
uses vcf tools (vcf-query) to query the vcf file for that variant and then
returns the genotype column. It is definitely doable, but messy (and I am
not a bioinformatics person).

We need this information in order to work out models of inheritance to
analyze whole exome sequencing data from lets say an affected proband and
his or her two unaffacted parents.

Many thanks,

-- 
Ricardo Parolin Schnekenberg
Genomics Research
Wellcome Trust Centre for Human Genetics
University of Oxford