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From dbSNP and GIAB gold standard NA12878, identify the high confident SNPs that can be used for allele-ratio queries

Howdy all, and thank you for your interest in this hackseq!

I'm hoping we can all introduce ourselves ourselves and start some conversations before we meet in Vancouver.

I am an assistant professor at Arizona State University: http://www.wilsonsayreslab.org. My research interests include understanding sex-biased genome evolution and how demography and selection shape genome-wide patterns of variation. In particular, my work has focused on characterizing evolution of the sex chromosomes across species.

I'm really looking forward to meet you all! In another week or so, I'll share some suggested readings ahead of our hackseq.

Best,
Melissa

Here's a plot of allele balance across a 1MB window of chrX in a 1000G female with emission thresholds depth > 10, allele balance > .1, min alt reads > 3.

Glossary of terms

Howdy all,

The broad goal of this hackseq group is, "Inferring sex chromosome and autosomal ploidy in NGS data".

There are a lot of people thinking about this, and in preparation for our hack-a-thon, please read and share current similar methods.

One to read through was just posted on BioRxiv:

GenomeScope: Fast reference-free genome profiling from short reads
http://biorxiv.org/content/early/2016/09/19/075978

Implementation: http://qb.cshl.edu/genomescope/, https://github.com/schatzlab/genomescope.git

Best,
Melissa

For individuals with no Y chromosome inferred, we will realign X and Y reads just to the X chromosome.

For individuals with a Y chromosome inferred, we will realign X and Y reads to both the X and the Y chromosome, but with shared X-Y regions masked out of the Y chromosome (so reads won't be split between the two chromosomes, and we can improve variant calling.)

I need to look into how the XTR aligns on the X and Y in samples with and without a Y chromosome.