aug2015 analysis team spiral genetics
TRANSCRIPT
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ANCHORED ASSEMBLYAccurate Structural Variant Detection Using Short-Read Data
AA
Bruestle, J.J. and Shekar, S.N.
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Methodology
Anchoring
AA
Anchor Assemblies
7 7 7
7
8 89 9
7
8
7
R1 R2
R3 R5
R8R7
R3 R6 R9
Read overlapassembly
Read Overlap Assembly
Remove Reference ReadsRead Correction
0
0 200 400 600 800 1000 1200
1000
2000
3000
4000
5000
K-m
er C
ount
Total K-mer Quality Score
K-mer Quality Score Distribution
A* error correction
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SV Comparison
Baylor College of Medicine, against Illumina, PacBio, Array, Nextera and BioNano
Program FDR Sensitivity
CNVnator 80.46% 22.62%
BreakDancer 58.89% 42.39%
Delly 55.13% 31.18%
Crest 14.87% 35.29%
Pindel 31.81% 56.70%
SVStat 1.79% 16.36%
Tiresias 69.04% 7.79%
Spiral 3.03% 42%
English et al. (2015), updated
AA
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Fosmid/PacBio validated SVsAA
Validated in collaboration by Malig, M, Eichler, EE et al.
Selected 15 high confidence SVs not previously detected in the 1000 Genomes Project
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PacBio validated SVs deleteAA
Chr Call Size (bp) Clones seq with PacBio
Validated by Micropeats
Validated by Dotplots
Call validated?
1 1026 2 2 2 yes
1 6375 2 2 2 yes
2 26838 2 2 2 yes
3 4184 1 1 1 yes
5 9507 2 2 2 yes
7 3013 1 1 1 yes
8 5157 2 1 1 yes
9 2883 1 1 1 yes
15 6051 2 2 2 yes
Malig, M, Eichler, EE et al. (Manuscript in preparation)
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PacBio validated SVs InsertsAA
Malig, M, Eichler, EE et al. (Manuscript in preparation)
Chr Call Size (bp) Clones seq with PacBio
Validated by Micropeats
Validated by Dotplots
Call validated?
1 1755 2 2 2 yes
1 3865 2 2 2 yes
8 2457 2 2 2 yes
8 1508 2 2 2 yes
13 2142 2 2 2 yes
X 1548 2 2 2 yes
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PacBio validation dotplotsAA
Malig, M, Eichler, EE et al. (Manuscript in preparation)
Chromosome 1
3.8kb insertion
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Chromosome 1
6.4kb deletion
PacBio validation dotplotsAA
Malig, M, Eichler, EE et al. (Manuscript in preparation)
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Chromosome 2
26.8kb deletion
PacBio validation dotplotsAA
Malig, M, Eichler, EE et al. (Manuscript in preparation)
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Ashkenazi Jewish Trio AA
Validated by Noah Spies using his program SV Viz
Chr2 Deletion Chr8 Insertion
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Reference
Chr 2 Deletion - FatherAA
Alternative
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Chr 2 Deletion - MotherAA
Alternative
Reference
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Chr 2 Deletion - OffspringAA
Alternative
Reference
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Chr 2 Deletion - VCF IdenticalAA
HG002 - Offspring chr2 34695829 T <DEL> 100 PASS NS=1;DP=51;SVTYPE=DEL;END=34736567;SVLEN=-40730 DP:AD 51:21,30
HG003 - Father chr2 34695829 T <DEL> 100 PASS NS=1;DP=55;SVTYPE=DEL;END=34736567;SVLEN=-40730; DP:AD 55:0,55
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Chr 8 Insertion - FatherAA
Alternative
Reference
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Chr 8 Insertion - MotherAA
Alternative
Reference
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Chr 8 Insertion - OffspringAA
Alternative
Reference
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HG0004
chr8 129739066 AATAAA 100 masking_present NS=1;DP=41;SVTYPE=INS; END=129739071;SVLEN=3404; DP:AD 41:28,13
Chr 2 Insertion - VCF IdenticalAA
GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCTGAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGTTTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGCTTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTGAGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAATAGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGCTATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACATCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATGCTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGGCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGCATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGTATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAGAGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAACTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGCAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTCTTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTACTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACTTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAGATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTGTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCCTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCAAAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAGCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTGACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTGATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGGGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTACCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAAACT
Mother
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GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCTGAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGTTTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAAGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAACAAACCATGTGGACGTGGCTTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTGAGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAATAGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGCTATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCCATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACATCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATGCTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGCATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGTATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAGAGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAACTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGCAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTCTTTAGAAAAGAAATTGTACGATCGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTACTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACTTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAGATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTGTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCCTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCAAGAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAGCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTGACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTGATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGGGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTACCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT
Chr 2 Insertion - VCF IdenticalAA
FatherHG003
chr8 129739066 AATAAA 100 masking_present NS=1;DP=47;SVTYPE=INS; END=129739071;SVLEN=3405;DP:AD 47:32,15
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Chr 2 Insertion - VCF IdenticalAA
HG002
chr8 129739066 AATAAA 100 masking_present NS=1;DP=18;SVTYPE=INS; END=129739071;SVLEN=3405;DP:AD 18:0,18
GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCTGAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGTTTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGCTTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTGAGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAATAGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGCTATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACATCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATGCTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGCATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGTATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAGAGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAACTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGCAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTCTTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTACTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACTTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAGATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTGTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCCTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCAAAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAGCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTGACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTGATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGGGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTACCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT
Offspring
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Chr 2 Insertion - VCF IdenticalAA
GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCTGAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGTTTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGCTTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTGAGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAATAGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGCTATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACATCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATGCTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGGCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGCATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGTATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAGAGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAACTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGCAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTCTTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTACTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACTTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAGATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTGTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCCTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCAAAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAGCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTGACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTGATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGGGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTACCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAAACT
Overlay - SNPs from both parents are present in the Offspring
GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCTGAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGTTTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAAGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAACAAACCATGTGGACGTGGCTTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTGAGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAATAGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGCTATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCCATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACATCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATGCTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGCATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGTATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAGAGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAACTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGCAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTCTTTAGAAAAGAAATTGTACGATCGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTACTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACTTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAGATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTGTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCCTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCAAGAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAGCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTGACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTGATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGGGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTACCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT
GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCTGAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGTTTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGCTTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTGAGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAATAGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGCTATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACATCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATGCTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGCATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGTATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAGAGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAACTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGCAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTCTTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTACTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACTTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAGATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTGTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCCTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCAAAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAGCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTGACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTGATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGGGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTACCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT
A
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What is GraphBWT?
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Core Technology to Make Anchored Assembly Feasible
• Needed a way to represent the read data that was graph based
• Fast search for variation from reference directly from the reads in a whole genome dataset
• Small enough footprint to store a read overlap graph of whole human genome in memory
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GraphBWT
• Technology for storing all of the reads that comprise the variation graph of a whole human genome
• Very compact to fit into memory (1.5 bytes per base)
• In memory, allows for extremely fast searches via subsequence
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Resulting technologies that use GraphBWT
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SpEC SV and Query
• SpEC: A lossless compression format that reduces BAM files to 50% of their original size and that can be analyzed with existing bioinformatics tools while compressed
• SpEC SV: SpEC that also includes a compact sequence index, known as a GraphBWT (3GB), which is a graph based representation of genomic variation
• SpEC Query: an API that reads SpEC SV files to enable rapid queries of sequence data via location or by a subsequence
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Create a SpEC SV File
Spiral’s SpEC SV File
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Query Times
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Samples, Variant calls SpEC Query using SpEC SpEC Query using SpEC SV
1 sample, 1 variant Milliseconds Milliseconds
1 sample, 1M variants 10 Minutes 5 Minutes
1000 samples, 1 variant 10-‐20 Minutes 10-‐20 Minutes
1000 samples, 1M variants 4 Days 2 Days
Variant types SNPs and Indels SNPs, Indels and SVs
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GraphBWT Technical Details
• Constant time traversal of k-mer graph for any sized k-mer
• Subsequence search linear with size of sequence
• Storage requirements grow linearly with size of novel sequence (i.e. variation)
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Use Cases for SpEC SV
• Search for evidence of variation in read data
• Compare graphs between individuals for unique variation
• Compare combined graphs of two groups
• Store variation, for example a reference genome
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