Questions tagged [plink]
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67
questions
4
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Can't convert my vcf to plink
I have run this and checked the .map for number of contigs and specified in the code plink --file vcf_corrected --chr-set 897 --make-bed --out output_file but keep ...
- 41
1
vote
1
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21
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Approach for manually adding genotype of two SNPs to plink files for 350 people?
I have a data set of ~350 humans, genotyped on an Illumina. I have bed, bim, and fam files for them. Because of difficulty genotyping them, the genotyping does not include rs7412 or rs429358. However,...
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1
vote
1
answer
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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 ...
- 11
0
votes
0
answers
77
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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 ...
5
votes
2
answers
451
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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 ...
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2
votes
0
answers
55
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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.
...
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0
votes
0
answers
75
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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 ...
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1
vote
0
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43
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 ...
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1
vote
1
answer
36
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 ...
- 111
1
vote
0
answers
45
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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 ...
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0
votes
1
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202
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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
111
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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
0
answers
127
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 ...
3
votes
1
answer
239
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 ...
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4
votes
1
answer
248
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)...
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