| Class | Description |
|---|---|
| AddOriginalAlignmentTags | |
| AnalyzeSaturationMutagenesis |
Process reads from a saturation mutagenesis experiment.
|
| AnalyzeSaturationMutagenesis.ReportTypeCounts | |
| ApplyBQSRArgumentCollection |
The collection of all arguments needed for ApplyBQSR.
|
| ApplyBQSRUniqueArgumentCollection |
The collection of those arguments for ApplyBQSR that are not already defined in RecalibrationArgumentCollection.
|
| BwaMemIndexImageCreator |
Create a BWA-MEM index image file for use with GATK BWA tools
|
| ClipReads |
Read clipping based on quality, position or sequence matching.
|
| ClipReads.ClippingData | |
| ClipReads.ReadClipperWithData | |
| CompareIntervalLists | |
| ConvertHeaderlessHadoopBamShardToBam |
This is a troubleshooting utility that converts a headerless BAM shard (e.g., a part-r-00000.bam, part-r-00001.bam, etc.),
produced by a Spark tool with --sharded-output set to true, into a readable BAM file by adding a header and a BGZF terminator.
|
| CountBases |
Calculate and print to the standard output the overall number of bases in a SAM/BAM/CRAM file
|
| CountReads |
Calculate and print to the standard output the overall number of reads in a SAM/BAM/CRAM file
|
| DownsampleableSparkReadShard |
A simple shard implementation intended to be used for splitting reads by partition in Spark tools
|
| FixCallSetSampleOrdering | |
| FixMisencodedBaseQualityReads | |
| FlagStat |
Accumulate flag statistics given a BAM file, e.g.
|
| FlagStat.FlagStatus | |
| GatherVcfsCloud |
This tool combines together rows of variant calls from multiple VCFs, e.g.
|
| GetSampleName |
Emit a single sample name from the bam header into an output file.
|
| HaplotypeCallerSpark |
********************************************************************************
* This tool DOES NOT match the output of HaplotypeCaller.
|
| IndexFeatureFile |
This tool creates an index file for the various kinds of feature-containing files supported by GATK (such as VCF
and BED files).
|
| LeftAlignIndels |
Left-aligns indels in read data
|
| PrintBGZFBlockInformation |
A diagnostic tool that prints information about the compressed blocks in a BGZF format file,
such as a .vcf.gz file or a .bam file.
|
| PrintReads |
Write reads from SAM format file (SAM/BAM/CRAM) that pass criteria to a new file.
|
| PrintReadsHeader | |
| SplitReads |
Outputs reads from a SAM/BAM/CRAM by read group, sample and library name
|
| Enum | Description |
|---|---|
| GatherVcfsCloud.GatherType |