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novoBreak: local assembly for breakpoint detection in cancer genomes
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Novobreak will get some duplicated results? #11

Open panxiaoguang opened 2 years ago

panxiaoguang commented 2 years ago

for example,

chr11   70503195    N   .   <TRA>   60  PASS    PRECISE;CT=5to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=GTCTTATGAGAAGTCCCAAGGAAGGGAGGGCCTTGTAGAAAGGTAGAGAACAAAAGACATAAAGTGACAGAAAGACAAAATGTGTTATTTTAACAAAAGGAAGCATTGGCCAGGTCTAGCAGATGGCTTCAGAACAAATGAAGCACATGTATATGAGGTTGAAACAACTAGGGGGATTGGAATTATTTTGAGAGTGAAAGAAGACATTATTAATGATTAATCCTGGGCTCTGGGAATACACCGTGACTGTCTTGTACAAATGAGACTTATGGTCACCCTAGCAATAGCTGACCCCACAGTGAAGGAAGTGCAGTGCCTTTGGGGTGGCGTCGTGGGAGTGTGGTTGATGCCCGCATCCTGGCTATTATAGGGGAGGTCATTATTGAAAACATTAAGAATTTGTACGGTGAAGGCAGAAACCTTGCCAGCTTTATTTAACCACTGCAGAATTAAAAGTGTTTTAGGTTAATACGTTGTATAACTATAACGTGTAAATATATCTACCATTTACAGAAGGGTTTGAATGAAAGAATGTACCAACCTCTTGTTTCATGAATTGAATAAATTGGGGACTTAGGTGTTTATTCCACAGCTGCTGCAGAGGAAGGGCTGATTTCTATTTAACCTGAGCATCCTTAGGTGCTTACTTTTACAGGCCTGGGGCAATTTTCAGGGCCACCAAGAGACTGCATGTGAAGAGCCTGACAGGCGAGTTCCAGGGCTGGGCTGCAGTGCCAGGCTTTGCATCCTCACAGGAGGAGGAAACGTGGCGCTTAATTGCTTCTCATGTATTCTGGGAATGCACATCACACTGAAGCAGCCCCTTTCCTCCCACTCCCTCCCTCCCTGCTCTCCCGCTCCAGAGGCCTGGGAAGGCAGAAAAGCCTGGCCCAGCAGGGTGCTTACAAGAGTGGGGGCCCTGTCCCTGTGCTGGTCTGTACAACTAGCTGCCCCAGTGC;SVTYPE=TRA;CHR2=chr2;END=16369412;SVLEN=0   GT  ./. E35384  contig2 size959 377 cov58.82    45  418 59.877990430622 418 59.877990430622 29  0   0   0   0   1826    464 60  464 60  49  0   0   0   0   564 4   580 3
chr11   70503199    N   .   <TRA>   60  PASS    PRECISE;CT=5to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=TTCATGAATTGAATAAATTGGGGACTTAGGTGTTTATTCCCCAGCTGCTGCAGAGGAAGGGCTGATTTCTATTTAACCTGAGCATCCTTAGGTGCTTACTTTTACAGGCCTGGGGCAATTTTCAGGGCCACCAAGAGACTGCATGTGAAGAGCCTGA;SVTYPE=TRA;CHR2=chr2;END=16369412;SVLEN=0 GT  ./. E35384  contig66    size157 2   cov1.91 492 7   60  7   60  30  0   0   0   0   1826    464 60  464 60  49  0   0   00  564 4   580 3
chr2    16369412    N   .   <TRA>   60  PASS    PRECISE;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=ACTGCAGAATTAAAAGTGTTTTAGGTTAATACGTTGTATAACTATAACGTGTAAATATATCTACCATTTACAGAAGGGTTTGAATGAAAGAATGTACCAACCTCTTGTTTCATGAATTGAATAAATTGGGGACTTAGGTGTTTATTCCACAGCTGCTGCAGAGGAAGGGCTGATTTCTATTTAACCTGTGCATCCTTAGGTGCTTACTTTTACAGGCCTGGGGCAATTTTCAGGGCCACCAAGAGACTGCATGTGAAGGGCCTGACAGGCGAGTTCCAGGGCT;SVTYPE=TRA;CHR2=chr11;END=70503195;SVLEN=0  GT  ./. E35384  contig4 size283 5   cov2.65 1826    464 60  464 60  49  0   0   0   0   45  418 59.877990430622 418 59.877990430622 29  0   0   0   0   580 3   564 4

actually they are the same events for :

chr2    16369412    16369413    chr11   70503195    70503196    N   377 +   -   TRA NovoBreak

I run manta, delly and svaba, they all get only one unique result, but Novobreak get four's