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hackseq / 2016_project_6

Inferring sex chromosome and autosomal ploidy in NGS data
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Call variants on X and Y #10

Open mathbionerd opened 7 years ago

mathbionerd commented 7 years ago

Thoughts: Make a model to test expectations for heterozygosity on X and Y under different scenarios

Genotype X_call Y_call
XX het none
XY hap hap
X0 hap none or partial_hap
XXY 1/2 het (Xm1Xm2 or Xm1Xp or Xm2Xp) or 1/2 hap (Xm1Xm1 or Xm2Xm2 or XpXp)* hap
XYY hap hap
XXX hap hap

But it should show increased depth, so edited above, and making a second table for relative depth:

Genotype X_depth Y_depth
XX 2x 0x
XY 1x 1x
X0 1x 0x (or partial)
XXY 2x 1x
XYY 1x 2x

Edit: XYY should not be het for Y (thanks to @pjie2 on twitter for pointing this out).

Phillip-a-richmond commented 7 years ago

platypus_vcf.txt

mathbionerd commented 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.

whitneywhitford commented 7 years ago

Folder on chrY 1kG phase3 release ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/chrY/

mathbionerd commented 7 years ago

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)