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-- ignores the rest of the labeled arguments following this flag
-- ignores the rest of the labeled arguments following this flag
-h displays help
-h displays help
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=== Decompose blocksub===
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Decomposes biallelic block substitutions into its constituent SNPs.
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#decomposes multiallelic variants into biallelic variants and write out to gatk.decomposed.vcf
vt decompose gatk.vcf -o gatk.decomposed.vcf
#before decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1
20 763837 . CA TG 50340.1 PASS AC=1;AN=2 GT 0|1
#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: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
One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.
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description : decomposes multialleic variants into biallelic in a VCF file. <br>
usage : vt decompose [options] <in.vcf> <br>
options : -o output VCF file [-]
-I file containing list of intervals []
-i intervals []
-? displays help
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