Questions tagged [imputation]

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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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1answer
23 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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1answer
27 views

Interpreting imputation result from GLIMPSE

I'm new to the imputation and phasing. 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 ...
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56 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 ...
0
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1answer
63 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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0answers
28 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, ...
3
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1answer
46 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 ...
1
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1answer
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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2answers
85 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 ...
3
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1answer
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, ...
3
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2answers
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 ...
6
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1answer
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 ...
4
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1answer
311 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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1answer
157 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 ...
6
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1answer
184 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, ...