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Illumina / manta

Structural variant and indel caller for mapped sequencing data
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Overlapping SVs occur in the same sample #278

Open jxcao98 opened 2 years ago

jxcao98 commented 2 years ago

Hello, I have applied manta on a mark duplicated BAM, but overlap SVs within the same sample were reported, like this:

SV1: 1 14436308 MantaDEL:1023:0:1:1:0:0 N <DEL> 999 Ploidy SVTYPE=DEL;SVLEN=-1933;END=14438241;CIPOS=0,0;CIEND=0,0;PRPOS=1.0;PREND=1.0;STRANDS=+-:44;SU=44;PE=32;SR=12;CIPOS95=0,0;CIEND95=0,0 GT:FT:GQ:PL:PR:SR 1/1:PASS:103:999,106,0:0,32:0,12

SV2: 1 14437072 MantaDEL:1023:0:1:3:0:0 N <DEL> 999 Ploidy IMPRECISE;SVTYPE=DEL;SVLEN=-1867;END=14438939;CIPOS=0,2;CIEND=0,2;HOMLEN=2;HOMSEQ=GT;PRPOS=0.3333333333333333,0.3333333333333333,0.3333333333333333;PREND=0.3333333333333333,0.3333333333333333,0.3333333333333333;STRANDS=+-:92;SU=92;PE=53;SR=39;CIPOS95=0,2;CIEND95=0,2 GT:FT:GQ:PL:PR:SR 1/1:PASS:218:999,221,0:0,53:0,39 Is this a reasonable result? Thank you!