31 results in 0.0033 seconds.
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Problems understanding .cov files in Plink
I’m doing a GWAS using plink and I’m trying to write a covariant file. I can't get my head around the format of a covariant file or even how to write... -
Need help with Plink map file
Hi,
I plan to phase my non-human organism genomic data using Shapeit2. I have recombination data available from literature, but I am struggling... -
Tools to check consistency between VCF genotypes & pedigree-stated sex/relationship?
X-post from Biostars.
We're currently trying to do identity checks on targeted genome sequencing data from ~15K samples. Our target panel... -
plink
hello everyone:
I am new to plink.
as I open the plink, it immediately run all of the lines I pasted below, and then I can't type anything... -
Error in plink: --homozyg-window-kb flag provisionally retired
Hi all,
I am really new to bioinformatics and tools such as PLINK.
I am running commands on plink data created from whole... -
Problem in merging 1000G and cases in Plink
I have some problems in stating the imputation. I work on imputation in case-only design. My reference panel is build37 of 1000G (phase 3) in VCF format... -
CNV analysis on Illumina NGS data with PLINK or other toolsets
I am looking to work with CNV calls made from WGS data by Illumina's 'new' Canvas & Manta tools. Has anyone used the standard PLINK approach for downstream... -
permutation with plink
Hello.
I'm working on data from illumina.
Now I'm doing permutation using plink with 36 core 60GB memory computers (linux).... -
Using PLINK to filter by phenotype
What I am trying to accomplish is very simple but am having great difficulty with this. I am working with .tped and .tfam files and would like to separate... -
haploview using plink files
Hello everyone,
I was wondering if anyone knows how to construct LD plots from plink data in haploview? I read the documentation and my files... -
Transforming .ped files back to .vcf with original chrom. name
I am currently working on trying to obtain the general statistics on a set of SNPs. I have the original vcf file that I used in Plink to analyze for LD,... -
PLINK Reference haplotype for Odd Ratio calculation
Hi all,
I have a simple PED/MAP file composed by ~900 individuals genotyped for 2 SNPs.
I performed a conditional haplotype... -
AnnaRu started a topic Mismatch between number of lines in plink .ped files and corresponding .map filein GeneralMismatch between number of lines in plink .ped files and corresponding .map file
I have a problem with a mismatch between the number of columns in a plink .ped file and the corresponding map file; when I try to produce a .bed file... -
plink2 to EIGENSOFT .geno conversion
Hi all,
I have used plink2 for my project, and now have a database of .ped, .map, .bim, .fam, etc... files. I am interested in trying a... -
Vcftools to convert vcf to plink, help
I have been trying to use vcftools to convert a vcf file into plink ped and map files.
If I separate my vcf by chromosome, then the it...
