2016_project_6

Inferring sex chromosome and autosomal ploidy in NGS data

Slide show here: https://docs.google.com/presentation/d/1OB2d_mu5zC742N_NKfzHjVpUm4BFtm5lUzniLLI--OQ/edit?usp=sharing

Publication Links

• chromosome X: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665286/
• chromosome Y: http://www.nature.com/nature/journal/v423/n6942/full/nature01722.html
• Repetitive mapping solutions: https://www.ncbi.nlm.nih.gov/pubmed/22124482

List of Goals: Assess X/Y ploidy and correct for misalignment

1. Extract input chromosomes - recommend chrX, chrY, chr19 - from BAM (can input any autosome)

2. Infer sex chromosome ploidy from WGS data relative to autosomal ploidy

   • XX
   • XY
   • XXY
   • X0
   • And all other combinations Use A. Quality B. Read Depth C. Allele Balance D. Ampliconic/Palindromic/CNV filter

   Typical expectations for heterozygous calls under different sex chromosome complements:

   Genotype	X_call	Y_call
   XX	het	none
   XY	hap	hap
   X0	hap	none or partial_hap
   XXY	het or hap	hap
   XYY	hap	hap
   XXX	het	none

   Note: Half of 47,XXY are paternal in origin -> do not expect het sites: http://humupd.oxfordjournals.org/content/9/4/309.full.pdf

   Expectations for depth under different sex chromosome complements:

   Genotype	X_depth	Y_depth
   XX	2x	0x
   XY	1x	1x
   X0	1x	0x (or partial)
   XXY	2x	1x
   XYY	1x	2x
   XXX	3x	0x

3. IF - If we infer there are no Y chromosomes in the sample, conduct re-mapping to increase confidence in X-linked alleles. Strip reads from X and Y Remap all X & Y reads to the X chromosome only Remove X and Y from the input BAM file Merge the empty Y and the remapped X chromosome into the BAM

4. Assessment of 1000 genomes high coverage data Compare SNV and CNV variant calling in 1000 genomes high coverage before/after running this pipeline Test how different alignment algorithms, parameters, and reference sequences affect variant calling in different regions of the X and Y Compare variant calling with the "Gold Standard" reference individual

Other goals: Because I think we have to address this if we want to get a really good handle on #2 given the extremely high copy number variable regions on X and Y - the ampliconic regions. Likely we will masking them out to infer #2, which will be easiest, but then we can have an extended goal to see characterize variations in these regions.

Known problems and complications

• High sequence identity between X and Y
• Higher amount of sequence repeats

Group Members