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

Question

[rafa.rios.50]

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

Answer 1

[Pierre Lindenbaum]

GATK VariantsToAllelicPrimitives https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_LeftAlignAndTrimVariants.php

Answer 2

[harold.smith.tarheel]

Or VCFLIB 'allelicprimitives'