Questions tagged [imputation]
The imputation tag has no usage guidance.
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Convert genotyping results to vcf or other plink formats
I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
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Does using a microarray chip that matches the chip used in training lead to higher explained variance of a polygenic score?
I'm trying to replicate an existing polygenic score (i.e. test the accuracy in a new sample), and want to know if matching the original study's microarray chip will improve the accuracy (that is, ...
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Does phasing improve imputation quality?
If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.
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How do I fix chromosome-specific Michigan Imputation Server error (Imputation on chromosome 14 failed. Imputation was stopped)
I am imputing human genome samples, all hg19, using the Michigan Imputation Server. The input of the data is one VCF per autosome, which each VCF containing a few dozen samples.
The samples within the ...
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Should genotype imputation be ancestry specific?
I'm wondering if imputation, specifically Beagle, needs a reference panel that matches the sample's ancestry group. For example, Beagle documentation suggests the 1000 Genomes Project phase 3 ...
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reliable and popular HLA imputation tools
Could someone recommend me popular and reliable tools for HLA imputation?
I'm starting my master thesis project and I will infer the HLA region of 2000 sample in a case-control study; I searched for ...
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correlation between imputed genotype and true genotype
There is a graph in the link https://odelaneau.github.io/GLIMPSE/rsquare_eur.html. This graph shows the imputation accuracy of certain MAF bins. Now I understand that $r^2$ is the correlation between ...
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Publicly available population specific reference panels
The publicly available reference panel for GWAS analysis is the 1000 genomes reference panel. The reference panel consists of several populations. However, I am searching for a population-specific ...
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Imputing small region of the genome
If I'm looking for a specific SNP in my SNP-Chip data and it isn't there, are there any tools that let me quickly impute that SNP from surrounding SNPs rather than running a lengthy 'whole chromosome' ...
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Missing value imputation method for gene expression data
I am new to working with gene expression data sets and am wondering what is the most standard or best way to impute missing values in a gene expression data? I got mine from the GEO database and the ...
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Confusing result from Sanger Imputation Service (Eagle v2.4 for phasing, PBWT v3.1 for imputation)
I ran my 23andMe data through the Sanger Imputation Service that uses Eagle v2.4 for phasing, PBWT v3.1 for imputation.
However, some aspects of the results are very confusing to me. Perhaps see #3 (...
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SNPs in LD in which populations?
I have 3 SNPs that are in LD in 'several' populations here:
https://www.ebi.ac.uk/gwas/variants/rs13078854#ld_panel_label
It's a pain to look at all (30) populations one by one to manually check if ...
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Chosing an imputation panel for SNP-Chip data?
I have about 1,000 SNP-Chip data (samples) that I'd like to impute over (for the purpose of having more rsIDs to match against GWAS data).
However, I don't know the ancestry of each sample / the ...
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Imputing 23andMe 3v data to v4 and v5?
The 23andMe version 3 data (v3) is now quite 'old' and new data is being collected on the updated v5 Illumina SNP-Chip (details here).
Is there an online service for imputing 23andMe v3 files to v4 ...
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Given a 'random' rsID, how can I find the closest (LD) SNP in a given set of SNPs?
I'm assuming that this is such a common question that I don't have to do my own imputation...
I have a SNP from a paper that is associated with a specific trait... Actually I have 8 of them:
https://...
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Topmed File Requirements
I am trying to run my VCF's through Topmed Imputation (https://imputation.biodatacatalyst.nhlbi.nih.gov/#!pages/home)
I am trying to make sure that I have the correct requirements for my file to be ...
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502
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imputed dosage values for vcf files
I have one more question related to genotype file. I submitted the job in michigan imputation server.
and my imputed dosage for chr 22 file is:
22 16050435 22:16050435:T:C T C . PASS
AF=0.00098;MAF=0....
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Interpreting imputation result from GLIMPSE
I'm following this tutorial of GLIMPSE for learning. I was expecting some extra SNPS coming from the 1000 genome reference in the resulting .vcf file. Though I understand the phasing in the output ...
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ERROR: Failed to allocate 18446744073709551596 bytes
I'm using Eagle 2.4.1 for phasing a vcf.gz file. Whenever I give the command it gives me the following error
...
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Tutorials on phasing and imputing low-coverage sequencing data
I am new to low-pass whole genome sequencing and have the basic idea of phasing and imputation. I have .vcf file after calling haplotypecaller tools from GATK. After searching the phasing and ...
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What is the best QC to do on imputed UK Biobank data?
I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have QC'd for missingness per individual and per SNP, sex discrepancy, ...
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Imputation of dog genotype
I am an undergrad working on a set of genotype matrix of dogs, it's in csv file format with information on only the each sample as rows, chromosome and its position as columns, and the rest of the ...
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REMC SNP annotations for transcriptome prediction - epiXcan
I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper:
https://www....
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Block wise protein imputation
I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The features of the date set are:
The data is perfectly balanced between blocks, with equal treatment ...
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Impute phenotype under some constraints
Errors happen frequently in the lab and I got one sample that we mixed one important information (the region of the sample) between two samples. Now we don't know which sample is from which region, ...
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How to filter info score post-imputation?
this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation?
I did imputation in Impute2 and am planning on using ...
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Order of batch effects removal, data imputation and library size normalization in scRNA-seq data
I am preprocessing scRNA-seq data. What is the best practice in use to run both ComBat for batch effects removal, data imputation (to mitigate dropout) and library size normalization?
I thought that ...
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Recommendations for missing value imputation - DNA methylation data
I'm looking for some options for imputation for a high-dimensional dataset of DNA methylation (bisulfite sequencing) data. Dimensions on the order of 50-100 samples x ~500,000 CpG loci/features.
I'...
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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 ...
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Filtering imputed GWAS SNPs based on a MAF difference of 10%
There are many posts on the web regarding QC steps pre and post-imputation.
Does applying below (new?) 10% MAF difference rule make sense, pitfalls?
Here is the process:
Get MAF for imputed set, ...
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