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Line 345: |
| vt decompose gatk.vcf -o gatk.decomposed.vcf <br> | | 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 <br> | + | 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 <br> | + | 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. | | 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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| vt decompose -s gatk.vcf -o gatk.decomposed.vcf <br> | | vt decompose -s 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 <br> | + | 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 |