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User: janhuang.cn

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janhuang.cn • 60
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Posts by janhuang.cn

<prev • 44 results • page 1 of 5 • next >
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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 9 days ago by janhuang.cn • 60
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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 9 days ago by janhuang.cn • 60
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Comment: C: SNPs that are merged in dbSNP
... Thank you very much. ...
written 10 days ago by janhuang.cn • 60
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SNPs that are merged in dbSNP
... I am analysing the 1000G VCF files, rs80314515 is not available in the VCF, but rs10204648 is available. dbSNP returns this message when I search rs80314515 ([https://www.ncbi.nlm.nih.gov/snp/?term=rs80314515][1]) rs80314515 has merged into rs10204648 I wonder if there is a data base about ...
1000g vcf merge snp written 11 days ago by janhuang.cn • 60 • updated 11 days ago by Kevin Blighe • 3.0k
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Comment: C: Extract the SNP list of a VCF file
... Thank you very much. ...
written 11 days ago by janhuang.cn • 60
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Comment: C: Extract the SNP list of a VCF file
... Thanks. This is very helpful. Is it possible to apply to vcf.gz? This command return the filename of VCF, if I apply it to vcf.gz file. ...
written 11 days ago by janhuang.cn • 60
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Comment: C: Extract the SNP list of a VCF file
... Combine with the command suggested by ATPoint, I used the below command to extract the list, extracting chr, pos and rsid. vcf2bed < foo.vcf | awk '{if (length($4) == 1 && length($5) == 1 || $1 ~ /^#/) print $0}'| cut -f1,3,4 > ids.txt But when I use my VCFs, I got an error as b ...
written 11 days ago by janhuang.cn • 60
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Comment: C: Extract the SNP list of a VCF file
... I want to the chr, pos, and rsid. ...
written 11 days ago by janhuang.cn • 60
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Extract the SNP list of a VCF file
... Is it possible to extract the list of all SNP (save as a .txt) of a VCF file? I do not want to convert it into .bed, and check the .bim, because the VCFs I have are large, and I have many of them. ...
vcf snp written 12 days ago by janhuang.cn • 60 • updated 11 days ago by Pierre Lindenbaum ♦ 99k
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Comment: C: loadling bcf2 file in plink
... I see. Thank you very much. ...
written 12 days ago by janhuang.cn • 60

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