Questions tagged [plink]
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58
questions
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14
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Proper formatting of .ped files, in order to run ADMIXTURE
I'm trying to run ADMIXTURE on some files I've generated using the Stacks pipeline. ADMIXTURE accepts .bed and .ped files, but when I try to pass the .ped file generated by Stacks to ADMIXTURE (v1.3.0)...
- 51
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14
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How to separate samples and phenotype code into separate columns in linux to create a phenotype file
I am trying to create a phenotype file for plink, and it's called merged.Phenotype.tsv. The format should be three fields: sample, sample (repeated), and phenotype number (1 for case and 2 for control)...
3
votes
1
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43
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Using QCTOOL v2 to process UK Biobank .bgen files - why so slow?
I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal?
My command is pretty basic; I’m filtering out a list of ...
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8
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Plink assigns all samples as control, when there are cases listed in .fam
My case and control samples are combined in one .bed. I changed my .fam file to include the phenotype value for the samples in the .bim, but they might be in a different order than listed in the vcf ...
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10
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How to replace values in .fam file corresponding to the case and control samples (IID) of my data set?
I have a .fam file, but because the vcf used to create the .fam has no phenotypical information, and the phenotypic value column had all -9, the .fam file does not distinguish which samples are case (...
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0
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21
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Assigning case and control label to different samples of large merged file to input into a plink 1.9.0 association test
I have a large vcf file with both case and control samples in the file. I am planning to input the vcf into the --assoc function of plink with the --fam parameter that contains a .fam file that ...
1
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1
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34
views
Converting Control and Case vcf files into a format that can be processed by plink 1.9.0
I have two vcf files, one containing samples with TP53 mutations, and one containing samples with no TP53 mutations. The vcf without the mutations is the control and the vcf with the mutations is the ...
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0
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17
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PLINK sanity check
I am a new user of PLINK and am analysing some SNP data for the first time.
After creating a .bim file with
$ plink --file my_data --make-bed
I notice that for ...
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0
votes
1
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81
views
How to extract a subset of individuals from a .bgen file?
I have 10,000 controls and 3000 cases and the .bgen file has genotype of 200,000 individuals. I would like to extract only those individuals from the .bgen file that are either cases or controls using ...
1
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1
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146
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Plink error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus
I am running an analysis in plink.
This is my first attempt at a QC and I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this ...
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1
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22
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Publicly available genotype / phenotype dataset?
I'm looking for publicly available genotype data (eg. 1000 Genomes or HapMap) that also has associated phenotypes (any traits). I'm wanting to use it as a test run for a GWAS pipeline. Does anyone ...
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41
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Linking UK biobank patient IDs with their corresponding genetic data
I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs.
I am trying to test with chromosome 5 as I have both bgen ...
- 21
0
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1
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127
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How to convert vcf to tbed/tfam and again convert it back to tbed/tfam to vcf using plink
When converting vcf to tbed/tfam format, I am getting error like
unrecognized flag<'--transpose'>
Code I used:
...
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19
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Association test to get p values and OR in plink2, and file input format
Are there any commands for association testing in plink2 which will output p-value and OR in the resulting output file? If so, what kind of file input do I need to use for such commands...a vcf.gz ...
1
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1
answer
41
views
Output of allelic association doesn't write the rsID
I'm using plink (1.9b5) to do allelic association. My problem is that my output does not write the rsID (SNP), it just writes a dot.
Output:
...
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1
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1
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764
views
Error: "fewer tokens than expected" while using --update-name flag in plink
I am trying to update my rsIDs in .bim file by using --update-name flag in plink but getting this error message. what could be the reason of it?
...
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45
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How do I remove allele annotations from SNP Ids in .bim file?
Hello every one i need help in editting my .bim file. So my .bim file looked like following. I want to convert the ids with chromosomal position from chr1_867635_C_T...
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1
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49
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Convert SNP data from GEO into PED and MAP files?
I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147
GEO provides data as SOFT ...
- 402
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27
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Is SNPRelate the goto package for PCA of SNP data in R?
I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?
Many thanks,
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248
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Nextflow: Runs without error, produce few but not all output files into output channel
I was trying to develop a pipeline using nextflow and plink. My code runs without any error, but got only two output files instead of 22 (one for each chromosome). Here is part my code block, any help?...
- 147
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368
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nextflow: Filter outputs of a process
How could I filter outputs of a process in the input of the next process? Filtering works fine in channel, but if I try to filter outputs I got compilation error. I tried as follows:
...
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2
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1
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203
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Nextflow: No signature of Method: chr() is applicable for argument types; unknown variable
I was trying to use plink in nextflow. My first process will split the input (single bed|bim|fam file) into 22 chromosomes (each with bed|bim|fam files) which would be used in subsequent processes. My ...
- 147
1
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0
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23
views
plink doesn't generate a sexcheck-file
I was executing the following command plink.exe --file GWAS --check-sex --noweb
Expecthing to get a plink.sexcheck file but I ...
0
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0
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48
views
Reliably create female and male individuals in a -ped file for plink
For a study I need some kind of "decoy" GWAS-data. For this I created a panel with some genes, the same ones as in the real data. From NCBI I fetch some of their SNPs and create my own ...
1
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1
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432
views
Making PLINK compatible files from VCF file without phenotype information
I have a big VCF file that I need to convert to, preferably, bed/bim/fam files that are readable by plink. Currently using plink 2. I am aware that this version of plink can be used to convert VCFs ...
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1
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0
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61
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Merging plink files with divergent allele codings
I have a number of plink files from different arrays (mixed Illumina and Affymetrix) that need to be merged. However, these use different allele codings, so trying to merge without fixing this causes ...
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1
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47
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Random GWAS data generator
I was wondering if there is a tool/script/program that randomly generates GWAS data. The purpose of such a tool would be to use it for educational purposes. So you generate some random .ped, .map and ...
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83
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GWAS phenotype data format and preprocessing
I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input.
I have control and ...
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2
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131
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Interpreting GWAS results with different settings
I did a bunch of GWAS analysis (linear model without covariates) with applying different quality controls. How to choose the optimal settings when filtering for minor allele frequency (maf), Hardy-...
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138
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plink: Error: ALT allele duplicates REF allele on line 37074 of .vcf file
I am working with the public WGS files from the HGDP from here: ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/
I want to convert the VCFs to plink binary format (bed, bim, fam). However, ...
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2
votes
2
answers
607
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Lifting from hg38 to hg37
I am having strange issues lifting this dataset to hg37 from hg38. I am using the HGDP WGS data from ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/. The data set split by chromosome, so I ...
- 143
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2
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1k
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plink: --update-name vs. editing the BIM
I am working with data from the HGDP public files. These are massive VCFs from whole genome sequencing. To begin with, I converted these to BEDs using plink (1.9). The next problem is that these files ...
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22
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GWAS Rooted PCA analysis problem
I'm fairly new to plink software and wanted to get some additional practice after doing several tutorials. I obtained the data from this paper (I'm not using this paper's methods) to do some QC with ...
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2
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1
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643
views
Converting aligned fasta to plink ped/bed
I have an alignment of multiple sequences in a FASTA file (output from MAFFT), for which I would like to simulate a phenotype using plink, but for that I need to have my alignment in a PED file or ...
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1
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259
views
Plink 1.9 equivalent of --score sum in Plink 2.0
I have previously performing Allelic scoring in Plink 1.9 using:
plink \
--score sum sumstats.txt\
However, it seems this has changed in Plink 2.0. What is the ...
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2
votes
1
answer
109
views
How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic)
The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on ...
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1
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187
views
How to simulate phenotype from real genetic data for GWAS purpose?
I'm trying to simulate binary phenotypes from the 1000 Genome Phase 3 datasets using gcta64 --simu-cc, but no success.
Everything seems to be going well, but in the end I get:
...
- 187
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56
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Why my bim file doesn't match to my ped file as the Plink documentation suggests?
Plink documentation about .bim says the columns 5 and 6 are the Allele 1 and Allele 2 respectively.
The documentation about the .ped in turn, says "...The first six fields are the same as those in a ....
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1
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59
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Question: How to simulate 100k samples having 40 million SNPs in a proportion of case:control=30:70?
Note: this question can also be found on Biostars
I need to perform a stress test in a GWAS tool and the duty demands a dataset (plink format) having 100 thousand samples, having 40 million SNPs in a ...
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938
views
Wrong format .ped in PLINK
I know that I don't have the correct format in my .ped file for PLINK but I don't know how to convert it.
My actual file is something like:
...
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357
views
Running IBD using PLINK --parallel (v2)
I have merged two huge .gen files with roughly 500k samples in total - around 3 TB.
I wish to run an IBD (identity by descent) check to identify if there are ...
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73
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Sibling vs Parent/Child relationship detection using whole-genome sequence data
I am analyzing a family-based whole-genome sequence (WGS) dataset. My identity-by-descent(IBD) analysis shows they share about 50% of their DNA. I think my pedigree structure may have gotten mixed up ...
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2
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674
views
How to compute LD for pairs of variants with Plink
I have a set of SNPs (single nucleotide polymorphisms) { S1, S2, ..., SN } from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By ...
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2
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1
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170
views
PLINK - Transposed BED file?
I'm currently working with the PLINK file system to store large amounts of genotype data.
The plain format consists of three files, two files for storing phenotype and marker information as well as ...
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1
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1
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1k
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Plink 1.9 --merge-list changing order of fam file
I am doing some whole-genome sequence analysis and to speed things up split the data into chromosomes and also into regions within those chromosomes. (So I have my dataset split into ~300ish files) I ...
- 445
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2
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73
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Calculate average parental genotype
I am interested in creating an averaged value for genotype across two parents:
E.g. Input (three unrelated couples, 1, 2 and 3):
...
- 133
2
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1
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195
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Parallel in PLINK for linear association for SNP effects
I am doing linear association calculations for SNP effects, I see it take a lot of time to do, does anyone have any experience in parallelizing this job. I have used ...
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0
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50
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What should I use as a reference file for clumping?
I'm new to using PLINK and I have 2 basic questions about clumping. I'm computing polygenic risk scores for psychiatric diseases and will be using the following command to clump:
...
2
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1
answer
349
views
Visualize PLINK pedigree files
Is there a pedigree viewer that works with PLINK pedigree files? I saw an old post by Pierre, but I don't see the script on his blog.
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245
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Error filtering SNPs with Plink
Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (...
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