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How to split Double or Multiple Nucleotide Polymorphisms (DNP) into Single Nucleotide Polymorphisms (SNP)?

Greetings,

I have a vcf file with some variants as the following:

NC_002516.2 6892 . GG AA 200.00 . . GT:CLCAD2:DP 1:0,59:59

NC_002516.2 45742 . CC TT 200.00 . . GT:CLCAD2:DP 1:0,49:58

NC_002516.2 41006 . CCT TTC 200.00 . . GT:CLCAD2:DP 1:0,79:79

I was wondering if there was a tool that could split those variants into SNPs, obtaining:

NC_002516.2 6892 . G A 200.00 . . GT:CLCAD2:DP 1:0,59:59

NC_002516.2 6893 . G A 200.00 . . GT:CLCAD2:DP 1:0,59:59

NC_002516.2 45742 . C T 200.00 . . GT:CLCAD2:DP 1:0,49:58

NC_002516.2 45743 . C T 200.00 . . GT:CLCAD2:DP 1:0,49:58

NC_002516.2 41006 . C T 200.00 . . GT:CLCAD2:DP 1:0,79:79

NC_002516.2 41007 . C T 200.00 . . GT:CLCAD2:DP 1:0,79:79

NC_002516.2 41008 . T C 200.00 . . GT:CLCAD2:DP 1:0,79:79

Thank you

snp variant calling vcf
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updated by Biostar Biostar • written by rafa.rios.50 • rafa.rios.50

2 answers

Or VCFLIB 'allelicprimitives'

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written by harold.smith.tarheel harold.smith.tarheel

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