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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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How to extract INS.DUP type REF and ALT sequence #646

Closed lixuenan closed 5 months ago

lixuenan commented 7 months ago

Operating system linux I call SV with PBSV call ,and I get some INS.DUP,BND,Now I want to get ALT DUP sequences ,but it does not appear in vcf file, How can I get this sequences? chr1 339052 pbsv.INS.DUP.19 C . PASS SVTYPE=DUP;END=339380;SVLEN=328 GT:AD:DP 0/1:6,5:11 chr1 339337 pbsv.INS.DUP.20 T . PASS SVTYPE=DUP;END=339450;SVLEN=113 GT:AD:DP 0/1:5,5:10

armintoepfer commented 5 months ago

This is not supported. Pinging @ctsa who is developing our pbsv2 successor