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#decomposes multiallelic variants into biallelic variants and write out to gatk.decomposed.vcf
#decomposes multiallelic variants into biallelic variants and write out to gatk.decomposed.vcf
vt decompose gatk.vcf -o gatk.decomposed.vcf
vt decompose gatk.vcf -o gatk.decomposed.vcf <br>
#before decomposition
#before decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567
1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567 <br>
#after decomposition
#after decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
1 3759889 . TA TAA . PASS OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
1 3759889 . TA TAA . PASS OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
1 3759889 . TA TAAA . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
1 3759889 . TA TAAA . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
1 3759889 . TA T . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567
1 3759889 . TA T . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567 <br>
One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.
#decomposes multiallelic variants into biallelic variants and write out to gatk.decomposed.vcf with the -s option.
#-s option splits up INFO and GENOTYPE fields that have number counts of R and A [[https://samtools.github.io/hts-specs/VCFv4.2.pdf VCFv4.2 section 1.2.2]] appropriately.
vt decompose -s gatk.vcf -o gatk.decomposed.vcf <br>
#before decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567 <br>
#after decomposition
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
1 3759889 . TA TAA . PASS AF=0.342;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
1 3759889 . TA TAAA . . AF=0.173;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
1 3759889 . TA T . . AF=0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567 <br>
One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.
One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.
