Save filter and annotat vcf + sqlite

[volyavi]

Hi,

It that possible to annotate a vcf and a sqlite file at the same time?

I would like to filter variants on some criteria. So I use openCravat filter and save it but I would like to use this filter for other analysis. Is that possible? Same question about the layout ( colones order in web interface).

Thank you again

Ivaylo

[rkimoakbioinformatics]

Hi, this coming release of OpenCRAVAT will have export/import feature for filters. Thus, for example, you will be able to do the following.

oc run input.vcf ... oc gui input.sqlite

You can create a filter and save it, then export it to a json file such as filter.json. Then,

oc gui input2.vcf -f filter.json -t vcf

This will produce input2.vcf.vcf with the filtered variants from the variants in input2.vcf.

Was this what you were asking about?

[volyavi]

Thank you,this (filter export) will be great.

also I would like to mixe vcf and sqlite annotation like this:

oc run input.vcf input2.sqlite 

The main idea is to keep previous annotation with personal notes ( on some variant) in input2.sqlite and to append the new variants with the oc annotation tools.

I try to do this but it did not work. May be I did on the wrong way ?

[rkimoakbioinformatics]

Mixing text files and sqlite files as input to oc run is currently not supported, but that is an interesting use case. We'll get back to you here with possible solutions.