User: Floris Brenk

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Floris Brenk790
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Posts by Floris Brenk

<prev • 165 results • page 1 of 17 • next >
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PCA matching controls with cases
... Hi there, I have a relatively small dataset of cases (n=~800) and a very large amount of controls (n=~8000) in plink format. Now I would like to have the case-control ration 1:3 for further analysis. I was wondering is there a method or are there scripts available that perform some kind of PCA matc ...
pca plink written 2 days ago by Floris Brenk790
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Answer: A: Duplicate ID in bed file
... Using --list-duplicate-vars you can identify the duplicates in the data [plink website identifying duplicates][1] And using --exlcude you can remove your snps [plink website removing snps][2] [1]: https://www.cog-genomics.org/plink/1.9/data#list_duplicate_vars [2]: https://www.cog-genomics.or ...
written 7 days ago by Floris Brenk790
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Output the call rate of genotypes in plink
... Hi all, I was wondering whether someone knows an easy solution to output the call rate per individual from a plink file. I know you can filter on the call rate using --mind, but I would like to have a list with the call rate per sample. I tried some coding myself by taking each sample by itself and ...
plink written 22 days ago by Floris Brenk790 • updated 22 days ago by chrchang5232.5k
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Making a vcf file from a subset of regions from gvcf files
... Dear all, We have a large exome sequencing (>8000) cohort and recently processed them. Now at the end of the line there are some weird results for a few genes. So I would like to recreate some of the final vcf files (all samples combined). However doing this for all samples will take really long ...
vcf gatk written 29 days ago by Floris Brenk790 • updated 26 days ago by aays60
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Comment: C: extract SNPs (rs.....) along with subject ID and pedigree ID in PLINK
... Maybe just use --recode this gives you a .ped file and here the ID is next to the SNPs that are in your region ...
written 7 weeks ago by Floris Brenk790
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... Yes just keep males and females in the same file and use as above described `plink --bfile Input_data --set-hh-missing --recode vcf --out Result_filename`. Then make sure you use the right chromosome name I remember just using X was fine and use shapeit in combination with hrc.r1.1.2016 ...
written 8 weeks ago by Floris Brenk790
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Comment: C: converting rows into columns and vice versa
... Here is it first mentioned in 2009 -> https://stackoverflow.com/questions/1729824/an-efficient-way-to-transpose-a-file-in-bash ...
written 9 weeks ago by Floris Brenk790
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Comment: C: converting rows into columns and vice versa
... How many samples do you have for your 11 million SNPs? You tried this? awk ' { for (i=1; i<=NF; i++) { a[NR,i] = $i } } NF>p { p = NF } END { for(j=1; j<=p; j++) { str=a[1,j] for(i=2; i<=NR; i++){ str= ...
written 9 weeks ago by Floris Brenk790
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Merge several association signals in a region and use as a phenotype
... Dear all, I got some case/control association signals in one locus and now want to perform a bit more advanced eQTL analysis in this region. I already did a standard single variant eQTL analysis and here not much interesting came out. Now I want to merge the association signals (assuming they are s ...
gwas riskscore written 9 weeks ago by Floris Brenk790 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: Chromosome Y imputation, any good reference panels?
... Ok thanks for your reply! As a follow up, are you aware of any tools that can identify the haplotype group based on plink data? ...
written 3 months ago by Floris Brenk790

Latest awards to Floris Brenk

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 5 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Scholar 6 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Student 9 months ago, asked a question with at least 3 up-votes. For Reformat minimac imputated files to plink file
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Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Gene Expression And Transcript Expression
Scholar 12 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Scholar 13 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
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Scholar 15 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Popular Question 16 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Appreciated 17 months ago, created a post with more than 5 votes. For A: Difference Between Gene Expression And Transcript Expression
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Popular Question 20 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 22 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 22 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Popular Question 22 months ago, created a question with more than 1,000 views. For SNP in Transcription factor binding site analysis
Popular Question 22 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 23 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Scholar 2.6 years ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: 1000 Genomes Ld Calculation
Scholar 3.2 years ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?

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