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Modify ID column in VCF file

Hello,

I have a vcf file that has the following first three columns:

CHROM POS ID

chr1 121 .
chr1 125 .
chr1 127 .
chr2 100 .

how can I change the Column "ID" so that it consists out of CHROM + ID like in the following example:

CHROM POS ID

chr1 121 chr1:121
chr1 125 chr1:125
chr1 127 chr1:127 chr2 100 chr2:100

Thank you all for your help! Max

snp vcf
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written by Figaro1993 • Figaro1993

1 answer

use bcftools annotate https://samtools.github.io/bcftools/bcftools.html#annotate

-I, --set-id [+]FORMAT

    assign ID on the fly. The format is the same as in the query command (see below). By default all existing IDs are replaced. If the format string is preceded by "+", only missing IDs will be set. For example, one can use
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written by Pierre Lindenbaum Pierre Lindenbaum

I tried it and it works. Thank you for the fast reply!

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written by Figaro1993 • Figaro1993

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