4.0.5.0
Tool documentation for GATK release 4.0.5.0
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MergeVcfs (Picard)
Combines multiple variant files into a single variant file.Inpu... -
MethylationTypeCaller (EXPERIMENTAL)
Identify methylated bases from bisulfite sequenced, methylation... -
MetricsReadFilter
Filter out reads that fail platform quality checks, are unmappe... -
ModelSegments (BETA)
Models segmented copy ratios from denoised read counts and segm... -
Mutect2
Call somatic SNVs and indels via local assembly of haplotypes ... -
NonChimericOriginalAlignmentReadFilter
Filters reads whose original alignment was chimeric. Catego... -
NonNFastaSize (Picard)
Counts the number of non-N bases in a fasta file.This tool take... -
NonZeroFragmentLengthReadFilter
Filter out reads with fragment length different from zero C... -
NonZeroReferenceLengthAlignmentReadFilter
Filter out reads that do not align to the reference Categor... -
NormalizeFasta (Picard)
Normalizes lines of sequence in a FASTA file to be of the same ... -
NotDuplicateReadFilter
Filter out reads marked as duplicate Category Read Fil... -
NotSecondaryAlignmentReadFilter
Filter out reads representing secondary alignments Category... -
NotSupplementaryAlignmentReadFilter
Filter out reads representing supplementary alignments Cate... -
OrientationBiasReadCounts
Count of read pairs in the F1R2 and F2R1 configurations support... -
OriginalAlignment
Number of alt reads with an OA tag that doesn't match the curre... -
OverclippedReadFilter
Filter out reads that are over-soft-clipped Category R... -
OxoGReadCounts
Count of read pairs in the F1R2 and F2R1 configurations support... -
PairedReadFilter
Filter out unpaired reads Category Read Filters ... -
ParallelCopyGCSDirectoryIntoHDFSSpark (BETA)
Parallel copy a file or directory from Google Cloud Storage int... -
PassesVendorQualityCheckReadFilter
Filter out reads failing platfor/vendor quality checks Cate... -
PathSeqBuildKmers
Builds set of host reference k-mers Category Metagenom... -
PathSeqBuildReferenceTaxonomy
Builds a taxonomy datafile of the microbe reference Categor... -
PathSeqBwaSpark
Step 2: Aligns reads to the microbe reference Category ... -
PathSeqFilterSpark
Step 1: Filters low quality, low complexity, duplicate, and hos... -
PathSeqPipelineSpark
Combined tool that performs all steps: read filtering, microbe ... -
PathSeqScoreSpark
Step 3: Classifies pathogen-aligned reads and generates abundan... -
Pileup
Prints read alignments in samtools pileup format Category ... -
PileupSpark (BETA)
Prints read alignments in samtools pileup format Category ... -
PlatformReadFilter
Keep only reads with matching Read Group platform Category ... -
PlatformUnitReadFilter
Filter out reads with matching platform unit attribute Cate...