Stack Exchange Network

Stack Exchange network consists of 175 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

  7. current community

    your communities

    more stack exchange communities

    company blog
Bioinformatics Beta

Questions tagged [impute2]

The tag has no usage guidance.

3 questions
info Newest Frequent Votes Active Unanswered
3
votes
1answer
47 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 ...
7
votes
3answers
943 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
83 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 ...