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Faizal-Eeman committed Jul 5, 2024
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146 changes: 146 additions & 0 deletions v5.2.0/404.html
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61 changes: 61 additions & 0 deletions v5.2.0/call-gSV.puml
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@startuml
skinparam SwimlaneTitleFontStyle bold

start

:==Normal BAM
---
Input Normal BAM;
:==Input Validation
---
Validate the input BAM and corresponding index file;
fork
if (run_discovery) is (true) then
split
:==DELLY gSV
---
Call germline SVs using DELLY
(BCF);
:==DELLY gCNV
---
Call germline CNVs using DELLY
(BCF);
:==QC
---
Quality Check variant calls;
:==Output Validation
---
Validate BCF output;
split again
:==Manta gSV
---
Call germline SVs using Manta
(VCF);
end split
else (false)
endif
stop

fork again
if (run_regenotyping) is (true) then
split
:==Regenotype gSV
---
Regenotype SVs
using DELLY gSV calls
(BCF);
note right: input\nmerged\ngSV sites
split again
:==Regenotype gCNV
---
Regenotype CNVs
using DELLY gCNV calls
(BCF);
note left: input\nmerged\ngCNV sites
end split

else (false)
endif
stop

@enduml
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162 changes: 162 additions & 0 deletions v5.2.0/contributors/index.html
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