Imputation Without A Reference Panel
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8.1 years ago

I would like to know if there are there any tools to impute missing SNPs for a resequencing dataset of hundreds of individuals for which there is no reference panel?

The closest I got is:

(1) in using a subset of the most complete individuals with the "include reference" MACH (http://www.sph.umich.edu/csg/abecasis/MaCH) option:

INCLUDE REFERENCE (e.g. HAPMAP) GENOTYPES TO YOUR DATASET:

If you select this option, you should simply create one large pooled dataset. Some individuals will have missing data and others will have much more complete genotyping information.

In addition to estimating the most likely genotype for each individual, you can use the command line options --dosage and --quality options to request additional information about each inferred genotype.

Other tools I looked at:

(2) in using Impute (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html):

We have proposed a simple and universal solution to this problem: we provide all available reference haplotypes to IMPUTE2, then let the software choose a "custom" reference panel for each individual to be imputed. There are several advantages to this approach

Beagle (http://faculty.washington.edu/browning/beagle/beagle.html) doesn't seem to mention options for including the reference in the input.

imputation snps • 6.0k views
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Mach and Beagle do not require a reference panel. You will known that if you try them once.

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8.1 years ago
pd3 ▴ 340

How many sites do you need to fill? Both IMPUTE2 and BEAGLE can be used without reference genotypes. Of course, the more "holes" (missing data) there are, the less accurate the method get.

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7.2 years ago
kumar.vinod81 ▴ 300

What command line to use for missing genotype imputation in MACH without a reference panel. Is this?

To estimate model parameters ...

prompt> mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.haplos --greedy --rounds 10 --prefix round1

To fill in missing genotypes ...

prompt> mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.haplos --greedy --errormap round1.erate --cross round1.rec --mle --mldetails

Or we have to left some commands......

Thanks

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