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Line 719: |
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| <div class=" mw-collapsible mw-collapsed"> | | <div class=" mw-collapsible mw-collapsed"> |
− | #converts in.bcf to tab format with selected INFO fields | + | #converts in.bcf to tab format with selected INFO and FILTER fields |
− | vt info2tab in.bcf -v -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT | + | vt info2tab in.bcf -u PASS -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT |
− | | |
| <div style="height:6em; overflow:auto; border: 2px solid #FFF"> | | <div style="height:6em; overflow:auto; border: 2px solid #FFF"> |
| + | INPUT |
| + | ===== |
| 20 17548608 . A AC . PASS CENTERS=vbi;NCENTERS=1;OLD_MULTIALLELIC=20:17548598:GAAAAAAAAAAAAA/GAAAAAAAAAAAA/GAAAAAAAAAAAAAA/GAAAAAAAAAA/GAAAAAAAAAAA/GAAAAAAAAAACAAA;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAACAAAG;EX_MOTIF=C;EX_MLEN=1;EX_RU=C;EX_BASIS=C;EX_BLEN=1;EX_REPEAT_TRACT=17548608,17548609;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=2;EX_RL=2;EX_LL=3;EX_RU_COUNTS=0,2;EX_SCORE=0;EX_TRF_SCORE=-14;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=14;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[A]AAAGAAGGAA;MDUST;LOBSTR | | 20 17548608 . A AC . PASS CENTERS=vbi;NCENTERS=1;OLD_MULTIALLELIC=20:17548598:GAAAAAAAAAAAAA/GAAAAAAAAAAAA/GAAAAAAAAAAAAAA/GAAAAAAAAAA/GAAAAAAAAAAA/GAAAAAAAAAACAAA;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAACAAAG;EX_MOTIF=C;EX_MLEN=1;EX_RU=C;EX_BASIS=C;EX_BLEN=1;EX_REPEAT_TRACT=17548608,17548609;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=2;EX_RL=2;EX_LL=3;EX_RU_COUNTS=0,2;EX_SCORE=0;EX_TRF_SCORE=-14;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=14;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[A]AAAGAAGGAA;MDUST;LOBSTR |
| 20 17548608 . AAAAG A . PASS CENTERS=ox1;NCENTERS=1;EX_MOTIF=AAAG;EX_MLEN=4;EX_RU=AAAG;EX_BASIS=AG;EX_BLEN=2;EX_REPEAT_TRACT=17548609,17548612;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=0.75;EX_RL=4;EX_LL=4;EX_RU_COUNTS=0,1;EX_SCORE=0.75;EX_TRF_SCORE=-1;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=13;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[AAAAG]AAGGAACTAC;MDUST;LOBSTR;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAA | | 20 17548608 . AAAAG A . PASS CENTERS=ox1;NCENTERS=1;EX_MOTIF=AAAG;EX_MLEN=4;EX_RU=AAAG;EX_BASIS=AG;EX_BLEN=2;EX_REPEAT_TRACT=17548609,17548612;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=0.75;EX_RL=4;EX_LL=4;EX_RU_COUNTS=0,1;EX_SCORE=0.75;EX_TRF_SCORE=-1;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=13;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[AAAAG]AAGGAACTAC;MDUST;LOBSTR;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAA |
− |
| |
| </div> | | </div> |
− | | + | OUTPUT |
− | CHROM POS REF ALT N_ALLELE EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2 | + | ====== |
− | 20 17548608 A AC 2 2 13 1 1 0 0 17548608 17548608 | + | CHROM POS REF ALT N_ALLELE PASS EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2 |
− | 20 17548608 AAAAG A 2 4 13 1 1 0 0 17548609 17548609 | + | 20 17548608 A AC 2 1 2 13 1 1 0 0 17548608 17548608 |
| + | 20 17548608 AAAAG A 2 1 4 13 1 1 0 0 17548609 17548609 |
| | | |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| usage : vt info2tab [options] <in.vcf> | | usage : vt info2tab [options] <in.vcf> |
| | | |
− | options : -v print variant CHROM,POS,REF,ALT,N_ALLELE [false] | + | options : -d debug [false] |
− | -d debug [false]
| |
| -f filter expression [] | | -f filter expression [] |
− | -t list of info tags to be extracted [] | + | -u list of filter tags to be extracted []-t list of info tags to be extracted [] |
| -o output tab delimited file [-] | | -o output tab delimited file [-] |
| -I file containing list of intervals [] | | -I file containing list of intervals [] |