docs/call-gsnp-flow.svg

<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="1113px" preserveAspectRatio="none" style="width:643px;height:1113px;background:#FFFFFF;" version="1.1" viewBox="0 0 643 1113" width="643px" zoomAndPan="magnify"><defs/><g><ellipse cx="321" cy="20" fill="#222222" rx="10" ry="10" style="stroke:#222222;stroke-width:1.0;"/><polygon fill="#F1F1F1" points="272,50,370,50,382,62,370,74,272,74,260,62,272,50" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="98" x="272" y="65.8081">Explicit intervals?</text><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="21" x="239" y="59.4058">Yes</text><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="15" x="382" y="59.4058">No</text><rect fill="#F1F1F1" height="102.1719" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="217" x="96.5" y="84"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="187" x="106.5" y="106.9951">run_SplitIntervals_GATK</text><line style="stroke:#181818;stroke-width:1.0;" x1="96.5" x2="313.5" y1="115.2969" y2="115.2969"/><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="195" x="106.5" y="131.4355">Split reference genome into up</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="13" x="106.5" y="145.4043">to</text><text fill="#000000" font-family="sans-serif" font-size="12" font-weight="bold" lengthAdjust="spacing" textLength="97" x="123.5" y="145.4043">scatter_count</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="79" x="224.5" y="145.4043">interval lists,</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="187" x="106.5" y="159.373">without subdividing any of the</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="89" x="106.5" y="173.3418">input intervals</text><rect fill="#F1F1F1" height="74.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="207" x="333.5" y="84"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="187" x="343.5" y="106.9951">run_SplitIntervals_GATK</text><line style="stroke:#181818;stroke-width:1.0;" x1="333.5" x2="540.5" y1="115.2969" y2="115.2969"/><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="175" x="343.5" y="131.4355">Split reference genome into</text><text fill="#000000" font-family="sans-serif" font-size="12" font-weight="bold" lengthAdjust="spacing" textLength="97" x="343.5" y="145.4043">scatter_count</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="75" x="444.5" y="145.4043">interval lists</text><line style="stroke:#181818;stroke-width:1.5;" x1="171" x2="495" y1="224.1719" y2="224.1719"/><rect fill="#F1F1F1" height="74.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="260" x="41" y="244.1719"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="240" x="51" y="267.167">run_HaplotypeCallerVCF_GATK</text><line style="stroke:#181818;stroke-width:1.0;" x1="41" x2="301" y1="275.4688" y2="275.4688"/><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="229" x="51" y="291.6074">Generate VCFs for each split interval</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="136" x="51" y="305.5762">using HaplotypeCaller</text><rect fill="#F1F1F1" height="60.2656" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="256" x="43" y="338.4063"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="213" x="53" y="361.4014">run_MergeVcfs_Picard_VCF</text><line style="stroke:#181818;stroke-width:1.0;" x1="43" x2="299" y1="369.7031" y2="369.7031"/><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="236" x="53" y="385.8418">Merge raw variants into whole VCF file</text><polygon fill="#98FB98" points="59.5,418.6719,282.5,418.6719,292.5,435.6563,282.5,452.6406,59.5,452.6406" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="203" x="69.5" y="439.8105">Per-sample raw VCF + index files</text><rect fill="none" height="408.3281" style="stroke:#000000;stroke-width:1.5;" width="320" x="11" y="462.6406"/><path d="M157,462.6406 L157,471.9375 L147,481.9375 L11,481.9375 " fill="none" style="stroke:#000000;stroke-width:1.5;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="136" x="14" y="476.6357">Recalibrate Variants</text><rect fill="#F1F1F1" height="74.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="300" x="21" y="498.9375"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="267" x="31" y="521.9326">run_VariantRecalibratorSNP_GATK</text><line style="stroke:#181818;stroke-width:1.0;" x1="21" x2="321" y1="530.2344" y2="530.2344"/><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="280" x="31" y="546.373">Generate Variant Quality Score Recalibration</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="136" x="31" y="560.3418">(VQSR) table for SNPs</text><rect fill="#F1F1F1" 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@startuml

skinparam ConditionEndStyle hline

start

if (Explicit intervals?) is (Yes) then
    :==run_SplitIntervals_GATK
    - - - -
    Split reference genome into up
    to **scatter_count** interval lists,
    without subdividing any of the
    input intervals;
else (No)
    :==run_SplitIntervals_GATK
    - - - -
    Split reference genome into
    **scatter_count** interval lists;
endif

split

:==run_HaplotypeCallerVCF_GATK
- - - -
Generate VCFs for each split interval
using HaplotypeCaller;

:==run_MergeVcfs_Picard_VCF
- - - -
Merge raw variants into whole VCF file;

#palegreen:Per-sample raw VCF + index files>

partition "Recalibrate Variants" {

:==run_VariantRecalibratorSNP_GATK
- - - -
Generate Variant Quality Score Recalibration
(VQSR) table for SNPs;

:==run_ApplyVQSR_GATK_SNP
- - - -
Filter SNPs based on VQSR table;

:==run_VariantRecalibratorINDEL_GATK
- - - -
Generate VQSR table for INDELs;

:==run_ApplyVQSR_GATK_INDEL
- - - -
Filter INDELs based on VQSR table;

}

#palegreen:SNP and INDEL recalibrated
variants + index files>

:==filter_gSNP_GATK
- - - -
Filter ambiguous variants with
customized Perl script;

#palegreen:Filtered germline
variants + index files>

detach

split again

:==run_HaplotypeCallerGVCF_GATK
- - - -
Generate GVCFs for each split interval
using HaplotypeCaller;

:==run_MergeVcfs_Picard_GVCF
- - - -
Merge raw variants into whole GVCF file;

#palegreen:Per-sample GVCF + index files>

detach

endsplit


@enduml

PlantUML version 1.2022.6(Tue Jun 21 17:34:49 GMT 2022)
(GPL source distribution)
Java Runtime: OpenJDK Runtime Environment
JVM: OpenJDK 64-Bit Server VM
Default Encoding: UTF-8
Language: en
Country: US
--></g></svg>