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#decomposes multiallelic variants into biallelic variants and write out to gatk.decomposed.vcf
#decomposes biallelic block substitutions and write out to decomposed_blocksub.vcf
vt decompose gatk.vcf -o gatk.decomposed.vcf
vt decompose gatk.vcf -o decomposed_blocksub.vcf
#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
#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 763838 . A G 50340.1 PASS AC=1;AN=2;OLD_CLUMPED=20:763837:CA/TG GT 0|1
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description : decomposes multialleic variants into biallelic in a VCF file. <br>
description : decomposes biallelic block substitutions into its constituent SNPs. <br>
usage : vt decompose [options] <in.vcf> <br>
usage : vt decompose_blocksub [options] <in.vcf> <br>
options : -o output VCF file [-]
options : -o output VCF file [-]
-I file containing list of intervals []
-I file containing list of intervals []
