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Why is START and END the same in the diploidSV.vcf.gz? #312

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robertzeibich opened this issue Jul 7, 2023 · 0 comments
Open

Why is START and END the same in the diploidSV.vcf.gz? #312

robertzeibich opened this issue Jul 7, 2023 · 0 comments

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@robertzeibich
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manta version: /manta/1.5.0

Why is START and END the same?

chr1 3260742 MantaINS:2:652:652:0:3:0 A 999 PASS END=3260742;SVTYPE=INS;CIPOS=0,5;CIEND=0,5;HOMLEN=5;HOMSEQ=TGATG;LEFT_SVINSSE
Q=TGATGGTGATGATAATGATAGTGATGGTGATGATGATGGTGGTGGTGATGGTGATGGTGATGGTGGTGGTGATGATGGTGATGGTGATGATGGTGGTGGTGATGATGGTGGTGGTGATGATGGTGATGGTGATGATGGTGATGGTGGTGATGATG
GTGGTGG;RIGHT_SVINSSEQ=GGTGGTGATGATGGTGATGGTGGTGATGATGATGGTGATGATGGTGATGGTGATGATGGTGATAATGATAGTGGTGATGATGGTGATGATGATAGTGATGATGATGGTGATGATGGTGATGGCGGCGATGATGG
TGATGATGATGGTGATGGTTGTGATGATGTTGGTGATGGTGGTGATGATGATGGCATGATGGCAGTGATTCAAG GT:FT:GQ:PL:PR:SR 1/1:PASS:105:999,108,0:0,14:0,24

What is the length of the insertion? I am planning to use the diploidSV.vcf.gz and only consider records with a PASS for my analysis. Should I filter on something else or should I be good to go.

Help would be highly appreciated.

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