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hackseq / 2016_project_6

Inferring sex chromosome and autosomal ploidy in NGS data
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Identify high confidence SNPs across X and Y #5

Closed Phillip-a-richmond closed 7 years ago

Phillip-a-richmond commented 7 years ago

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

mathbionerd commented 7 years ago

My concern about using the GIAB gold standard is that we'll then have downstream ascertainment bias by the population of that individual.

mathbionerd commented 7 years ago

This will be combined into the variant calling issue (https://github.com/hackseq/2016_project_6/issues/10), including calling SNPs from the data and inferring read balance.