Questions tagged [plink]

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1answer
30 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 ...
0
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2answers
66 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
votes
1answer
35 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
vote
1answer
146 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 ...
1
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2answers
58 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
votes
1answer
53 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 ...
0
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0answers
34 views

GWAS Retrieve Target Sample from a whole set of samples and PRS in PRSice tool

I am trying to calculate the polygenic risk score (PRS) for the Target Samples in GWAS. I only have the bed/bim/fam file Plink format, after I calculate the SNP effect. Does anyone know how to ...
1
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0answers
37 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
votes
1answer
108 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.
1
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0answers
158 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 (...
6
votes
2answers
5k 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
votes
1answer
84 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
votes
1answer
634 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
votes
3answers
561 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
votes
1answer
820 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
vote
1answer
1k 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, ...
5
votes
2answers
502 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
votes
3answers
521 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, ...