Lumpy with Gemini

[Phillip-a-richmond]

Hello, I see that LUMPY is coming from the same lab as GEMINI, so I was wondering if there is a workflow for running annotating and filtering variants called by LUMPY.

Ideally, the pipeline would look like this:

1. Call variants with Lumpy on a BWAmem mapped bam file
2. Genotype variants using SVtyper to get homozygous/heterozygous calls, and quality scores
3. Run GEMINI to only focus on deletions first, annotating against genes, and through inheritance modes.

I'm currently doing 1 and 2, but 3 is in development stage using a couple different parsing and filtering scripts in combination with ANNOVAR. As I move my pipeline entirely to GEMINI for small variant annotation and prioritization, I'd like to also move my large variants in that direction.

Thanks for any help and input! This work is on human genomes for the diagnosis of rare genetic disorders.

Cheers, Phil

[ryanlayer]

Phil,

Since this is not really an issue, please email me at ryan dot layer at gmail dot com do discus.

Ryan

On Feb 17, 2017, at 10:58 AM, Phillip Richmond notifications@github.com wrote:

Hello, I see that LUMPY is coming from the same lab as GEMINI, so I was wondering if there is a workflow for running annotating and filtering variants called by LUMPY.

Ideally, the pipeline would look like this:

Call variants with Lumpy on a BWAmem mapped bam file Genotype variants using SVtyper to get homozygous/heterozygous calls, and quality scores Run GEMINI to only focus on deletions first, annotating against genes, and through inheritance modes. I'm currently doing 1 and 2, but 3 is in development stage using a couple different parsing and filtering scripts in combination with ANNOVAR. As I move my pipeline entirely to GEMINI for small variant annotation and prioritization, I'd like to also move my large variants in that direction.

Thanks for any help and input! This work is on human genomes for the diagnosis of rare genetic disorders.

Cheers, Phil

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