SNPid or chromosomal number and position in vcf
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3 months ago
Nai ▴ 20

How to replace . in SNP.txt with SNPid or chromosomal number and position in vcf

VCF SNP • 461 views
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no one will answer because no one knows what's in SNP.txt

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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

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get a file rs# CHROM:POS and use join to merge both files. https://linuxconfig.org/join

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I don't have this file rs #CHROM:POS

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I don't have this file rs #CHROM:POS which is related to my SNP.txt

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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.

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