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SVTYPE=BND on the same chromosome #114

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Knnnk opened this issue Apr 17, 2024 · 2 comments
Open

SVTYPE=BND on the same chromosome #114

Knnnk opened this issue Apr 17, 2024 · 2 comments

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@Knnnk
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Knnnk commented Apr 17, 2024

Hi, there. In TIDDIT 's output VCFs, there are lots of BND type SVs, which both breakpoints on the same chromosome. What does this mean? Should I be possible to interpret those same-chr-breakpoints as traditional type SVs? as other breakpoints SV callers such as GRIDSS?

@Knnnk
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Knnnk commented Apr 17, 2024

Here is an example:

Chr2    148356  SV_264_1        N       ]Chr2:158417]N  15      BelowExpectedLinks      SVTYPE=BND;REGIONA=148356,148604;REGIONB=158107,158417;LFA=1,4;LFB=1,4
;LTE=0,3;CTG=.    GT:CN:COV:DV:RV:LQ:RR:DR        0/1:2:14.056224899598394,8.32811880679709,35.20257234726688:0:3:0.13636363636363635,0.03571428571428571:12,1
1:19,21
Chr2    148680  SV_2625_1       N       ]Chr2:158291]N  50      PASS    SVTYPE=BND;REGIONA=148680,148803;REGIONB=158238,158291;LFA=7,13;LFB=7,13;LTE=0,0;CTG=G
TTATAGACCCATTCCTGATGAATGACATTCAGGGTCTACCAGGTATAGACCCATCCATAATGACATACTCCAAGGGTCTGCTAAGTCTAGACATATCACTGAGGACGAACTCCCAGGGTCACCAGATATAGACCCATCCTTGATGACAGACTGCCAGG
ATCTACCAGGTATATACTCATTCCTGACGACTGACTCTC     GT:CN:COV:DV:RV:LQ:RR:DR        0/1:2:27.669354838709676,7.9079792674225535,42.27777777777778:0:0:0.09302325581395
349,0.018518518518518517:13,35:26,38
Chr2    158291  SV_2625_2       N       N[Chr2:148680[  50      PASS    SVTYPE=BND;REGIONA=148680,148803;REGIONB=158238,158291;LFA=7,13;LFB=7,13;LTE=0,0;CTG=G
TTATAGACCCATTCCTGATGAATGACATTCAGGGTCTACCAGGTATAGACCCATCCATAATGACATACTCCAAGGGTCTGCTAAGTCTAGACATATCACTGAGGACGAACTCCCAGGGTCACCAGATATAGACCCATCCTTGATGACAGACTGCCAGG
ATCTACCAGGTATATACTCATTCCTGACGACTGACTCTC     GT:CN:COV:DV:RV:LQ:RR:DR        0/1:2:27.669354838709676,7.9079792674225535,42.27777777777778:0:0:0.09302325581395
349,0.018518518518518517:13,35:26,38
Chr2    158417  SV_264_2        N       N[Chr2:148356[  15      BelowExpectedLinks      SVTYPE=BND;REGIONA=148356,148604;REGIONB=158107,158417;LFA=1,4;LFB=1,4
;LTE=0,3;CTG=.    GT:CN:COV:DV:RV:LQ:RR:DR        0/1:2:14.056224899598394,8.32811880679709,35.20257234726688:0:3:0.13636363636363635,0.03571428571428571:12,1
1:19,21

Should I just go along these records? or something useful is behind?

@Knnnk
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Knnnk commented Apr 17, 2024

I am also wondering that REGIONA=6819607,6819746;REGIONB=6819997,6820101; record in the TIDDIT output VCFs.
Does these mean the confidence interval region of the both breakpoints separately? Should I use the exact points of SV or these 2 intervals, which one is more reasonable or acceptable?
Thanks

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