Questions tagged [impute2]

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1000 genomes missing SNPs on chr X in GRCh38

I am trying to get a reference together for imputation using the 1000 genomes data set. The GRCh38 version of the data set was made available earlier this year, but seems to be missing a significant ...
3
votes
1answer
59 views

IMPUTE2 missing filter option

I went through the manuals and can't find the meaning of the below flag: -filt_rules_l 'filter==0' Here is the link to manual for this flag: filt_rules_l Can ...
8
votes
3answers
2k views

How to convert the .vcf (imputed) file with GT:GP format to GT:DS?

I have the genotyped data from impute2 output in .gen format (imputed to 1000G P3). The file has genotype posterior probabilities (GP:3 values per variant). I have converted .gen to .vcf using qctools ...
7
votes
1answer
138 views

Imputing missing genotypes from separate genotyping panels

What is the current standard for imputing missing genotypes between two genotyping panels? I have two populations genotyped using two different panels (A & B), and I would like to impute all the ...