Open mathbionerd opened 7 years ago
For now we'll work on platypus (should be able to multi-thread this), and we can add another variant caller later.
Will also add CNV calls, in addition to SNVs.
Folder on chrY 1kG phase3 release ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/chrY/
One goal is to increase accuracy of variant calling in individuals where we think there is no Y chromosome (stripping X and Y reads and remapping just to the X chromosome).
Does anyone have ideas for how we can improve variant calling when we have a Y chromosome present? We can consider re-mapping using different mapping parameters just between the X and Y optimized for the different regions (e.g., X-degenerate, ampliconic, X-transposed)
Thoughts: Make a model to test expectations for heterozygosity on X and Y under different scenarios
But it should show increased depth, so edited above, and making a second table for relative depth:
Edit: XYY should not be het for Y (thanks to @pjie2 on twitter for pointing this out).