Questions tagged [plink]

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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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1answer
29 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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1answer
35 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: ...
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1answer
19 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
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1answer
46 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 ...
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1answer
111 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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0answers
9 views

Common QC parameters for SNP chip data in PLINK

How do you set QC measurements? Seems very subjective. Is there a right way to set: 1) individual call rate, 2) SNP call rate, 3) minor allele frequency (MAF), and 4) linkage disequilibrium (LD) in ...
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0answers
47 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 ...
1
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1answer
41 views

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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2answers
166 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 ...
2
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1answer
57 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 ...
1
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1answer
393 views

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 ...
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2answers
62 views

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): ...
2
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1answer
79 views

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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0answers
39 views

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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1answer
200 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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0answers
208 views

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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2answers
8k 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, ...
2
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1answer
105 views

How to create artificial or dummy phenotype data

I have whole genome sequence (human) data (SNP data), but don't have phenotype data ready for any traits yet. Hopefully, I will get real phenotype data soon. To run GWAS (genome-wide-association study)...
2
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1answer
823 views

removing indels in plink

I have data in Plink format. I removed Indels using --snps-only command in Plink, but still some snps are as below: rs58119544;rs5746975 0 16915280 T A ...
4
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3answers
819 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 ...
4
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1answer
1k views

LD analysis in PLINK based on reference and a SNP list

I'm new to PLINK and genetics, and getting confused with two PLINK commands for LD analysis: plink --bfile hapmap --r2 --ld-window-r2 --ld-snp-list --ld-window <...
1
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1answer
2k views

Using PLINK to find SNPs in LD (Linkage Disequilibrium) with another set of SNPs

I have a list of SNPs (index SNPs). As my tagging SNPs, I want to use SNP data from here. The data has the following column headers: Chromosome, Position, MarkerName, Effect_allele, ...
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2answers
689 views

PLINK clump behavior on missing SNPs?

I have a long list of autoimmune-associated SNPs, and I want to boil it down so that I get one SNP representing each LD block. I chose to use PLINK's --clump option for this. I'm roughly following ...
4
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3answers
773 views

Is there any difference between SNPs 'AG' and 'GA' in association analyses?

I am using plink to check the association between a phenotype and the SNPs of a gene. plink says the phenotype is significantly associated with a SNP on that gene, and when I check the SNP alleles, ...