User: dp0b

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dp0b20
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Posts by dp0b

<prev • 11 results • page 1 of 2 • next >
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Convert VCF dosage file into dosage only file
... Hi, Is it possibly to only output dosages from a generated vcf dosage file from minimac? Input format is ##fileformat=VCFv4.1 ##filedate=2017.7.5 ##source=Minimac3 ##contig= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL ...
vcf dosage minimac written 8 weeks ago by dp0b20 • updated 7 weeks ago by trausch730
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Gemma linear mixed model analysis with second grm format
... Hi I have been trying to run a univariate linear mixed model using GEMMA. However I was hoping to use a grm I have made else where- it is the second in grm format. The first few lines are as as follows 1 1 8.923316e-01 1 2 -5.544370e-02 1 3 1.903249e ...
software error gemma gsl gwas written 8 weeks ago by dp0b20
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Estimate recombination rate from linkage map
... Hi Simple question but just want to clarify how to estimate recombination rate from a genetic linkage map for a region. Recombination rate is cM/Mb so for a linkage map like below, so recombination for each snp is cM-previous cM/((position-prev position)/1000000) If I wish to estimate recombinat ...
linkage map physical map recombination written 5 months ago by dp0b20
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Eagle phasing and minimac imputation
... Hi, I wish to use eagle phasing and minimac imputation to impute to whole genome sequence. I have successfully phased my genotypes using eagle but Im struggling to read them into minimac. Minimac will tell me there are no marker overlaps between the target and reference, when there definitely is. ...
eagle minimac imputation genotypes phasing written 6 months ago by dp0b20
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scatterplotmatrix subscript labels
... Hi, I am using the car package in R to complete a scatterplot matrix with linear regression lines. I wish the column names on diagonal to be in subscript for some of the characters, is there a way I can incorporate expression into var labels? scatterplotMatrix(inbred[1:4],smooth = FALSE,ylim=c ...
R car scatterplot written 8 months ago by dp0b20 • updated 8 months ago by WouterDeCoster21k
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Fastphase cluster determination
... Hi, I want to determine the number of haplotype clusters there are in my dataset using fastphase. The results are meant to produce a _kselect file, but this never happens and fastphase always uses a K15 for the model. This is what I have been running- I wanted to test the number of clusters from 5 ...
cluster genotypes fastphase written 12 months ago by dp0b20 • updated 4 days ago by Gennady Khvorykh30
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Ancestral alleles in sheep
... Hi, I was hoping to examine several sheep populations for selection signatures and was hoping to use the iHS method. From what I can see the ancestral and derived alleles are required but these are unknown in sheep? How do you proceed with this type of analyses if the ancestral alleles are unknow ...
ihs selection signatures ancestral alleles written 14 months ago by dp0b20
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Comment: C: Calculate LogR ratio and BAF from X and Y intensities
... Thank you very much for your help. Is there a recommendation for choosing the baseline sample? ...
written 15 months ago by dp0b20
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Comment: C: Calculate LogR ratio and BAF from X and Y intensities
... Apologies I have attached the final report format. I was hoping to complete CNV analysis. ...
written 15 months ago by dp0b20
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Calculate LogR ratio and BAF from X and Y intensities
... Hi, Does any one have a recommendation of a method or a program to convert X and Y intensities from a genotyping final report text file to their Log R ratio and B allele frequency estimates. The LRR and BAF were not provided in the final report and I dont have access to Illumina Beadstudio. I was ...
R baf genotypes intensity written 15 months ago by dp0b20 • updated 15 months ago by Irsan6.3k

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Popular Question 5 months ago, created a question with more than 1,000 views. For Calculate LogR ratio and BAF from X and Y intensities

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