Questions tagged [imputation]
The imputation tag has no usage guidance.
15
questions
1
vote
1answer
33 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 ...
1
vote
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....
0
votes
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 ...
0
votes
0answers
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
votes
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 ...
1
vote
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
votes
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
vote
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....
4
votes
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
votes
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
votes
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
votes
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
votes
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'...
7
votes
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
votes
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, ...
