Questions tagged [plink]

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0 answers
17 views

Problem with Calculating Polygenic Risk Score (PRS) in Plink

I've been struggling with constructing a PRS score. In the pics you can see how my summary stats and my target data look like. Target Data Summary Stats I've tried the following code which should be ...
0 votes
0 answers
66 views

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 ...
3 votes
1 answer
175 views

Polygenic Risk score calculation using vcf files

I have about 750 vcf files and I am looking to generate a Polygenic Risk Score for each individual. I am planning to use either PLINK or LDPhred to generate a Risk Score. I have phenotype information ...
5 votes
2 answers
252 views

Converting VCF format to text for use with PLINK and understanding column mapping

I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I'm facing the problem that I seem to be unable to use it in ...
2 votes
0 answers
33 views

INDELS in PLINK files converted to VCF

I want to compare/validate variants called from sequencing data with array (plink format) variant data. I converted the plink files (.bim, .bed, and .fam files) with plink1 to vcf files. ...
0 votes
0 answers
57 views

Correctly coding indels for ped/map files in plink and VCF

I have a challenge with how to correctly code indels in plink (I plan to convert my binary file set to VCF and use it for lift over in downstream analysis). For instance, my dataset has an indel with ...
1 vote
0 answers
38 views

PLINK linear association testing command with an interaction and 2 covariates term

I am trying to write the right command for my association testing using PLINK 1.9 but I could not find a clear answer so far and not sure how to wrtie it correct. I have genotype variants called and ...
1 vote
1 answer
32 views

Finding linkage disequilibrium when I have a kinship matrix but not pedigree

I have a bunch of samples of a non-model organism divided in two groups: parental generation and offspring. I do not have a pedigree so I do not actually know who is a parent of who, and which are the ...
2 votes
1 answer
1k 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: ...
3 votes
0 answers
187 views

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)...
1 vote
0 answers
43 views

Project PLINK eigenvector from one group on top of another group

I have 1 .bcf file called with individuals from two groups, one which is my samples, another which is a reference panel. Due to my samples having a limited amount ...
0 votes
2 answers
2k views

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 ...
0 votes
1 answer
161 views

Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9

I downloaded the following vcf file from https://www.internationalgenome.org/. http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502....
2 votes
0 answers
96 views

Input for --score in PLINK 1.9 when generationg PRS using GWAS summary statistics

I'm conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics. It is known that the GWAS will give BETA and OR for ...
1 vote
1 answer
59 views

Output of allelic association doesn't write the rsID [closed]

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: ...
4 votes
1 answer
457 views

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 ...
1 vote
2 answers
907 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 ...
1 vote
0 answers
120 views

Converting from VCF to PLINK while maintaining the SNP names from the VCF file

Just as the title says, I am working in PLINK 1.9 trying to convert the following VCF into a PLINK file (binary or not either is fine), while maintaining the SNP names from the VCF file. I am on ...
1 vote
0 answers
82 views

Parsing PLINK recombination genetic map

I have a Plink genetic map with 4 columns: Chromosome, rs-snp, Map(cM), Position(bp) and approximately 8,000 lines find the recombination rate [Rate(cM/Mb)] from a HapMapII genetic map of 4 columns: ...
12 votes
2 answers
17k views

Converting VCF file to PLINK bed/bim/fam files

I am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, ...
1 vote
1 answer
674 views

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 ...
0 votes
0 answers
43 views

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 ...
0 votes
1 answer
771 views

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: ...
1 vote
1 answer
100 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 ...
1 vote
1 answer
776 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 ...
0 votes
1 answer
51 views

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 ...
0 votes
0 answers
118 views

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 ...
2 votes
1 answer
233 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 ...
0 votes
1 answer
469 views

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: ...
2 votes
2 answers
1k views

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 ...
1 vote
1 answer
885 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 ...
1 vote
1 answer
194 views

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 ...
1 vote
1 answer
2k 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? ...
1 vote
1 answer
103 views

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...
0 votes
0 answers
36 views

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,
1 vote
1 answer
73 views

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 ...
1 vote
1 answer
572 views

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?...
3 votes
1 answer
1k views

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 ...
1 vote
0 answers
34 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 ...
1 vote
0 answers
91 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 vote
0 answers
139 views

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 ...
0 votes
0 answers
202 views

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 ...
1 vote
2 answers
246 views

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-...
6 votes
4 answers
3k views

Convert rs ID of one hg build to rs IDs of another build

I have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150 as of the time of this post). Is there any ID mapping ...
2 votes
1 answer
1k 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 ...
1 vote
0 answers
33 views

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 ...
0 votes
1 answer
453 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: ...
0 votes
1 answer
146 views

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 ....
1 vote
1 answer
65 views

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 ...
1 vote
0 answers
623 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 ...