Slide show here: https://docs.google.com/presentation/d/1OB2d_mu5zC742N_NKfzHjVpUm4BFtm5lUzniLLI--OQ/edit?usp=sharing
- 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
-
Extract input chromosomes - recommend chrX, chrY, chr19 - from BAM (can input any autosome)
-
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 |
-
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
-
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.
- High sequence identity between X and Y
- Higher amount of sequence repeats
| Name | github ID | |
|---|---|---|
| Madeline Couse | mhcouse@gmail.com | @Madelinehazel |
| Bruno Grande | bgrande@sfu.ca | @brunogrande |
| Eric Karlins | karlinser@mail.nih.gov | @ekarlins |
| Tanya Phung | tnphung@ucla.edu | @tnphung |
| Phillip Richmond | phillip.a.richmond@gmail.com | @Phillip-a-Richmond |
| Tim Webster | timothy.h.webster@asu.edu | @thw17 |
| Whitney Whitford | whitney.whitford@auckland.ac.nz | @whitneywhitford |
| Melissa A. Wilson Sayres | melissa.wilsonsayres@asu.edu | @mwilsonsayres |