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2.9 years ago
Nai
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How to replace . in SNP.txt with SNPid or chromosomal number and position in vcf
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version 2.3.6
version 2.3.6
no one will answer because no one knows what's in SNP.txt
Sorry, Here SNP.txt is converted .vcf file for MatrixEQTL. The format is: id Genotype1 Genotype2 Genotype3 Genotype4 Genotype5 Genotype6 rs1457723673 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 rs779258992 1 1 2 2 1 1 1 1 2 1 1 1 2 1 3 1 2 1 1 1 1 1 1 1 1 1 3 1 rs1366371903 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 0 1 1 1 1 0 1 0 1 1 1 rs150969722 1 1 1 1 1 3 0 1 0 0 0 0 0 0 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 1 1 0 0 rs1351390918 1 1 1 1 1 1 1 1 1 0 1 1 1 0 2 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0 1 1 1 rs1363828207 1 1 1 1 3 1 1 1 1 0 1 0 1 0 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 . 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 . 1 1 1 1 1 1 2 1 1 0 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 3 1 1 1 1 1 1 1 1 1 . 1 1 1 1 0 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 . 1 1 1 1 1 1 1 3 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
These dots which don't have SNPid I want to replace as Chromosomal Position
get a file
rs# CHROM:POSand usejointo merge both files. https://linuxconfig.org/joinI don't have this file rs #CHROM:POS
I don't have this file rs #CHROM:POS which is related to my SNP.txt
How To Get Chromosome Position Given Rs Number?
I want to add RSID and chromosome position in SNPMATRIX.txt. In my file ID column has "." which I want to replace in text file.