Questions tagged [imputation]

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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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3 votes
1 answer
56 views

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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1 vote
0 answers
98 views

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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  • 13
2 votes
2 answers
67 views

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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3 votes
1 answer
28 views

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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2 votes
2 answers
52 views

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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0 votes
1 answer
97 views

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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3 votes
0 answers
51 views

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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1 vote
1 answer
50 views

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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1 vote
1 answer
108 views

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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1 vote
1 answer
91 views

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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60 views

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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0 votes
1 answer
101 views

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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1 vote
0 answers
44 views

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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3 votes
1 answer
49 views

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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1 vote
1 answer
58 views

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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  • 796
4 votes
2 answers
94 views

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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3 votes
1 answer
47 views

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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  • 4,622
3 votes
2 answers
2k views

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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  • 31
6 votes
1 answer
1k views

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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  • 1,733
4 votes
1 answer
328 views

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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  • 367
7 votes
1 answer
162 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 ...
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  • 841
6 votes
1 answer
197 views

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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