2021-11-16-21 Best Practices Meeting Notes

Date

18 Oct 2021

Elaine to send link to new GSD reference genome.
Elaine to schedule Reuben Buckley to present at a future meeting
Kuffel, Gina (NIH/NCI) [C] to send out Buckley paper.
Kuffel, Gina (NIH/NCI) [C] to set up presentation with Shaying's group for next meeting.

Item	Who	Notes
Welcome & Introductions	Gina Kuffel, Shaying Zhao
Pan Cancer Study Intro	Shaying Zhao	Breed prediction pipeline The 15TB harmonized reads are generated from cases with matched tumor and normal samples both passing our comprehensive quality control measures, including breed validation and prediction using our software provided
Canine MHC-I Genotyping Software	Yuan Feng
Canine Breed Prediction Pipeline	Kun-Lin Ho
Committee Goals	Gina	Variant filter file Some of the filters are not well understood by the group A discussion is needed to identify overlap and differences in variant calling filter files being used by various groups Dependent on genome best practices for calling germ-line mutations Best Practices publication Initial Outline on Box: https://nih.app.box.com/folder/137612017625 Elaine to potentially take the lead on this initiative A milestone driven outline with dates and assigned tasks is needed Set to begin work on this effort by mid August Target date for submission is October 1, 2021

EO- Link to Michigan pipeline will be available soon. I can share with group when I have it.

RC- About to do sequencing on a chunk of dogs, the imputation paper could be a great reference.

EO- Helpful with low-pass sequencing.

EO- There will be a release of all variants. Everything will be re-called since they aligned to the new GSD reference.

EO- We can have Reuben Buckley attend the meeting next time and give a Q & A. He is also in the alignment group.