Biopet User Manual
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Pipelines
Basty (Snp typing)
Bam2Wig
Carp (chip-seq)
Flexiprep (QC)
Gears (Metagenome)
Gentrap (RNA-seq)
Kopisu (CNV Calling)
Mapping (Alignment)
Sage
Shiva (variantcalling)
TinyCap (smallRNA)
Toucan (Annotation)
Tools
AnnotateVcfWithBed
BaseCounter
BastyGenerateFasta
BedToInterval
BedtoolsCoverageToCounts
BiopetFlagstat
CheckAllelesVcfInBam
DownloadNcbiAssembly
ExtractAlignedFastq
FastqFilter
FastqSplitter
FastqSync
FindOverlapMatch
FindRepeatsPacBio
GvcfToBed
MergeAlleles
MergeTables
MpileupToVcf
PrefixFastq
SageCountFastq
sagetools
SamplesTsvToConfig
SeqStat
SquishBed
SummaryToTsv
ValidateFastq
ValidateVcf
VcfFilter
VcfToTsv
VcfWithVcf
VepNormalizer
WipeReads
Release notes
0.7.0
0.6.0
0.5.0
0.4.0
0.3.2
0.3.1
Release notes Hotfix 0.3.1
0.3.0
Developer
Getting Started
Code Style
Example Dependecies
Example Pipeline
Example Tool
Example Pipeable
Scala docs
Biopet User Manual
Docs
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Release notes »
0.3.1
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Release notes Hotfix 0.3.1
A bug was found in de variant calling of gentrap. In this hotfix this is fixed
The graph building in Flexiprep was incorrect, this is fixed now
Read the Docs