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Why is Beagle v5.4 (imputation) not giving Allele Frequencies (AF) and DR2 in my output?
written by Olivia •Hi there! I have just imputed some low-coverage (<4x) whole genome sequencing samples using a WGS reference panel (>10x) and Beagle v5.4: ``` java -jar …
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linkage disequilibrium and haplotype analysis of GWAS .
written by gdeep.14 •Hi all, I have GWAS data. I have my data in 22 chromosome files in plink format. I have imputed genotype with Sanger imputation server. …
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How to impute missing SNPs of genotypic data of plant species, without having HapMap reference pane…
written by Abbas.M •hello all, I have a SNP genotype data of 228 accessions of cotton, on which I want to do GWAS. The genotype data has a …
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Getting centimorgan map units for 1000 Genomes data
written by devenvyasI have imputed VCFs, which I imputed using Beagle for 1000G reference sites (http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/). From these, I have a bed/bim/fam file that I made using …
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Error in GWAS using GenABEL package
written by jaafari.omidHello dears all, Actually I am running a plink data set (of a fish species) for GWAS using GenABEL package in R. The plink files …
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How to determine the haplotypes using Beagle
written by akangI have two datasets one has genotype data for 30 SNPs and one has genotype data for 29 SNPs.I want to impute for the missing …
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Phylogenetic tree in Adegenet
written by akangI am using a R package called adegenet to plot the nj tree from plink files. In my plink file (input.raw) FID and IID are …
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PLINK --update-name command error due to multiple SNPs with same chr:pos but different rs numbers i…
written by dam4lHi, I have a data file containing autosomal SNPs imputed from the 1000 genomes data. The SNPs in my file are named as chr:pos but …
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Request for BEAGLE tutorial
written by akang<p>Could someone please do a tutorial for BEAGLE(https://faculty.washington.edu/browning/beagle/beagle.html) imputation starting from plink ped and map files? It would be a great help to many including …
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extract SNPs from compressed PLINK files
written by NBHello, I have a large imputed data set, each file, divided by chromosome and I have a list of 58K SNPs to extract from the …
I just saw, this can you please provide a link to the format that you have?