How to perform imputation analysis between masked SNPs and ground truth

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2.8 years ago

raalsuwaidi ▴ 100

Hi all,

I have a vcf file that I am aiming to impute using IMPUTE2. I will mask some selected SNPs. My question is since I have the ground truth and the imputed result, how do I evaluate the quality of the imputation?

GWAS SNPs IMPUTE2 • 847 views

ADD COMMENT • link updated 2.8 years ago by LauferVA 4.5k • written 2.8 years ago by raalsuwaidi ▴ 100

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read the impute2 manuscript, or other articles on masked results. the impute2 algorithm will generate these for you on a by chromosome or by block or by input file basis (cant remember which)

ADD REPLY • link 2.8 years ago by LauferVA 4.5k

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Thank you so much. This makes sense.

ADD REPLY • link 2.8 years ago by raalsuwaidi ▴ 100

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yeah no problem. that is how the quality metrics are being calculated - they take a snp that they actually have genotyped, and impute it.

then, they check to see how accurate they were. this serves as a useful estimate for nearby variants nearby that have the same characteristics (that actually are only imputed).

ADD REPLY • link 2.8 years ago by LauferVA 4.5k

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