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bahlolab / linkdatagen

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Notes #1

Open trickytank opened 2 years ago

trickytank commented 2 years ago

Research question 1:

GATK UnifiedGenotyper current status. What alternatives are there?

Data types (set of SNPs):

SNP chip data
NGS data (VCF)

Use a universal file for SNPs and NGS. Has TOP/BOT, Genetic Map position, frequencies.

UF.hg19, UF.hg38 has 1.6M SNPs.

Research question 2:

Can we increase number of SNPs?

Global screening array (Illumina
gnomAD

Research question 3

Documentation,
number of SNPs,
(something) of genetic maps postions
(something) of frequencies

RQ4

UF.hg38 genetic maps. How many valid?