search

tonydisera / gene.iobio

An iobio app for examining gene variants
22 stars 4 forks source link

Misscaled gene model #114

Closed AlistairNWard closed 9 years ago

AlistairNWard commented 9 years ago

If only alignments are selected, the coverage is shown, but the gene model is not scaled correctly. Also, if only the alignments are uploaded, we should probably call variants by default.

AlistairNWard commented 9 years ago

Also, if we default to a trio, we should call on all bam files and so can still show the Prioritization matrix.

AlistairNWard commented 9 years ago

One other observation. If I select three BAM files and no VCF files, we see the coverage for all three (misscaled gene model). If I call with freebayes, I see that variants are called (e.g. the number), but no variants are actually displayed. This is observed on local and remote files.

tonydisera commented 9 years ago

Another great catch, Al. I have fixed the coverage chart scaling problem when only bam file provided. I still need to change gene.iobio to automatically call freebayes variants.

tonydisera commented 9 years ago

Oh yeah. I was able to see the problem on the trio of alignments. That is fixed now. Also, when user clicks on 'call from alignments' link, all variant cards will have variants called. The feature matrix will display and the inheritance mode will be determined. Are you okay with going this route instead of automatically calling variants as discussed in yesterday's lab meeting?

AlistairNWard commented 9 years ago

Yep, that sounds great to me.

On Wed, Sep 16, 2015 at 5:04 PM, Tony Di Sera notifications@github.com wrote:

Oh yeah. I was able to see the problem on the trio of alignments. That is fixed now. Also, when user clicks on 'call from alignments' link, all variant cards will have variants called. The feature matrix will display and the inheritance mode will be determined. Are you okay with going this route instead of automatically calling variants as discussed in yesterday's lab meeting?

— Reply to this email directly or view it on GitHub https://github.com/tonydisera/gene.iobio/issues/114#issuecomment-140920493 .