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User: janhuang.cn

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janhuang.cn • 10
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Posts by janhuang.cn

<prev • 16 results • page 1 of 2 • next >
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Keep one SNP for duplicate SNPs
... I have converted vcf file to bed files, and there are some duplicate SNPs. I would like to remove the duplicate SNPs, but keep one. For example, if rs1234 appears 5 times, I want to keep only one record (maybe the first one). Right now I used `--write-snplist` to get the snplist of the bed file, a ...
duplicate snp written 4 hours ago by janhuang.cn • 10
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Comment: C: ld matrix in plink
... Thank you very much. ...
written 4 hours ago by janhuang.cn • 10
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Comment: C: ld matrix in plink
... It returns Error: --ld-snp/--ld-snps/--ld-snp-list cannot be used with the --r/--r2 matrix output modifiers. ...
written 4 days ago by janhuang.cn • 10
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ld matrix in plink
... I am using the below command to generate an LD matrix in plink plink --r2 --bfile bfilename --ld-snp-list samplesnp.txt --ld-window-r2 0.8 --out samplesnp_ld but I want to export a matrix format, instead of the default table format. Instruction from plink webpage has the below explanation. It ...
matrix ld written 4 days ago by janhuang.cn • 10 • updated 4 days ago by chrchang523 • 2.5k
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Comment: C: Duplicate ID in bed file
... I used the `--list-duplicate-vars` to generate a list of duplicated SNPs, but it does not contain the one reported as dulicate in the analysis. ...
written 8 days ago by janhuang.cn • 10
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Duplicate ID in bed file
... I am using PLINK v1.90b3s 64-bit (17 Jun 2015) to generate a LD matrix from 1000G VCF file for a long list of SNPs. I use this command to convert VCF to bed file plink --vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --make-bed --out binary_fileset I then use t ...
bed duplicate id written 11 days ago by janhuang.cn • 10 • updated 11 days ago by Floris Brenk • 790
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Comment: C: Fail to open file in plink
... I see. Thank you. I put the hapmap1.map in the plink folder. ...
written 15 days ago by janhuang.cn • 10
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Fail to open file in plink
... I am new to plink, and I am following this tutorial. [http://zzz.bwh.harvard.edu/plink/tutorial.shtml#t2][1] But I cannot even open the file. I am using a PLINK 1.9 on Windows, 64 bit. I have put the hapmap1.ped and hapmap1.map in the folder which I store PLINK. I used the below command to add th ...
ped open file written 15 days ago by janhuang.cn • 10 • updated 15 days ago by Ram ♦ 12k
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Comment: C: Obtain the LD matrix from a list of SNP
... I downloaded the 1000 Genomes phase 3 VCF files from this FTP folder [ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/]. I wonder if the one named " " covers chr 1-22? I suspect "wgs" means whole genome, but it seems to me the file size not that big, comparing to the separated files of ch ...
written 18 days ago by janhuang.cn • 10
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Comment: C: Obtain the LD matrix from a list of SNP
... If I have only two lists, each with less than 10 SNPs, I can manually search on Ensemble. But I have more than a hundred lists, and each list may have different number of SNPs. I have two purposes: 1) To generate the LD matrix for each list of SNPs; 2) To identify SNPs with R2>= 0.8 within each ...
written 4 weeks ago by janhuang.cn • 10

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