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User: janhuang.cn

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janhuang.cn • 150
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Posts by janhuang.cn

<prev • 52 results • page 1 of 6 • next >
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Comment: C: How to extract proxy SNPs using 1000G vcf for a list of SNPs
... But I got the similar error message no matter I put .gz or not. plink --vcf ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --r2 --ld-window-r2 0.8 --ld-snp rs157595 Error: Failed to open ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes ...
written 7 months ago by janhuang.cn • 150
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Comment: C: How to extract proxy SNPs using 1000G vcf for a list of SNPs
... Error: Failed to open ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf. I got an error when using --vcf for gzipped vcf ...
written 7 months ago by janhuang.cn • 150
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How to extract proxy SNPs using 1000G vcf for a list of SNPs
... I would like to find the proxy SNPs (r2>0.8) for a list of SNPs. I have a long list, so I do not want to manually check and download from LDlink. I think plink and/or vcftools can do the job. But I came across some problems. I download the 1000G phase3 vcf (gzziped) from the ftp folder: [ftp://f ...
1000g proxy vcftools snp plink written 7 months ago by janhuang.cn • 150 • updated 7 months ago by chrchang523 ♦ 5.6k
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Comment: C: Illumina Human Methylation EPIC array annotation
... Thanks. The column heading says "UCSC_RefGene_Name: Target gene name(s), from the UCSC database. *Note: multiple listings of the same gene name indicate splice variants". But is there any information on how they (UCSC or Illumina) annotate it? For example, cg18478105 (chr20:61847650) was on YTHDF1 ( ...
written 10 months ago by janhuang.cn • 150
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Illumina Human Methylation EPIC array annotation
... I used the R package *IlluminaHumanMethylationEPICanno.ilm10b4.hg19* to extract the annotation of the CpGs in my data. I wonder if there is any documentation on how Illumina define these annotations? Is it solely based on the distance from the loci? Thank you very much. ...
dna methylation epic array annotation written 10 months ago by janhuang.cn • 150 • updated 10 months ago by Charles Warden ♦ 7.3k
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Comment: C: Infinium Methylation SNP
... Thank you very much ...
written 24 months ago by janhuang.cn • 150
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Comment: C: Infinium Methylation SNP
... How is full capture sequence defined? ...
written 24 months ago by janhuang.cn • 150
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Infinium Methylation SNP
... I am using `IlluminaHumanMethylation450kanno.ilmn12.hg19` package to obtain the SNP-associated probe information (probe_rs, probe_maf). The [reference manual][1] says > In addition to the SNP information provided by Illumina, we have added independent information on the overlap of the 450k wit ...
overlap snp cpg written 24 months ago by janhuang.cn • 150 • updated 24 months ago by andrew.j.skelton73 ♦ 5.8k
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Comment: C: SNPs that are merged in dbSNP
... Using the "Send to" function to download is very slow. RsMergeArch.bcp.gz is available in the dbSNP FTP folder: [ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/][1] [1]: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/ ...
written 2.0 years ago by janhuang.cn • 150
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Comment: C: Downloading synonyms for dbSNP rsids
... The above link is expired. The RsMergeArch.bcp.gz is now available here: [ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/][1] [1]: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/ ...
written 2.0 years ago by janhuang.cn • 150

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Popular Question 7 months ago, created a question with more than 1,000 views. For Extract the SNP list of a VCF file
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