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20 763838 . G GA 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
#decomposes biallelic clumped variant and write out to decomposed_blocksub.vcf
#decomposes biallelic clumped variant and write out to decomposed_blocksub.vcf and add phase set information in the genotype fields
vt decompose_blocksub -p gatk.vcf -o decomposed_blocksub.vcf <br>
vt decompose_blocksub -p gatk.vcf -o decomposed_blocksub.vcf <br>
#before decomposition
#before decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor normal
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor normal
1 159030 . TAACCTTTC TGACCTTTT 0.04 . AF=0.5 GT 0|0 1|1 <br>
1 159030 . TAACCTTTC TGACCTTTT 0.04 . AF=0.5 GT 0/0 1/1 <br>
#after decomposition
#after decomposition
1 159031 . A G 0.04 . AF=0.5;OLD_CLUMPED=1:159030:TAACCTTTC/TGACCTTTT GT:PS 0|0:159031 1|1:159030
1 159031 . A G 0.04 . AF=0.5;OLD_CLUMPED=1:159030:TAACCTTTC/TGACCTTTT GT:PS 0|0:159031 1|1:159030
