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Decomposes biallelic block substitutions into its constituent SNPs.
Decomposes biallelic block substitutions into its constituent SNPs. <br>
There is now an additional option -a which decomposes non block substitutions into its constituent SNPs and indels. (kindly added by [[https://github.com/holtgrewe holtgrewe@github]]) <br>
There is no exact solution and this decomposition is based on the best guess outcome using a Needleman-Wunsch algorithm. <br>
todo: rename program?
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#decomposes biallelic block substitutions and write out to decomposed_blocksub.vcf
#decomposes biallelic block substitutions and write out to decomposed_blocksub.vcf
vt decompose_blocksub gatk.vcf -o decomposed_blocksub.vcf
vt decompose_blocksub gatk.vcf -o decomposed_blocksub.vcf <br>
#before decomposition
#before decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
20 763837 . CA TG 50340.1 PASS AC=1;AN=2 GT 0|1
20 763837 . CA TG 50340.1 PASS AC=1;AN=2 GT 0|1 <br>
#after decomposition
#after decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
20 763837 . C T 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CA/TG GT 0|1
20 763837 . C T 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CA/TG GT 0|1
20 763838 . A G 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CA/TG GT 0|1
20 763838 . A G 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CA/TG GT 0|1
#decomposes biallelic clumped variant and write out to decomposed_blocksub.vcf
vt decompose_blocksub -a gatk.vcf -o decomposed_blocksub.vcf <br>
#before decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
20 763837 . CG TGA 50340.1 PASS AC=1;AN=2 GT 0|1 <br>
#after decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
20 763837 . C T 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CG/TGA GT 0|1
20 763838 . G GA 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CG/TGA GT 0|1
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