4.0.1.0
Tool documentation for GATK release 4.0.1.0
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MeanQualityByCycleSpark (BETA)
MeanQualityByCycle on Spark Category Diagnostics and Quality C... -
MergeBamAlignment (Picard)
Merge alignment data from a SAM or BAM with data in an unmapped BAM fil... -
MergeSamFiles (Picard)
Merges multiple SAM and/or BAM files into a single file. This tool is ... -
MergeVcfs (Picard)
Combines multiple variant files into a single variant file.Inputs ... -
MethylationTypeCaller (EXPERIMENTAL)
Identify methylated bases from bisulfite sequenced, methylation-aware B... -
MetricsReadFilter
Filter out reads that fail platform quality checks, are unmapped and re... -
ModelSegments (BETA)
Models segmented copy ratios from denoised read counts and segmented mi... -
Mutect2 (BETA)
Call somatic SNVs and indels via local assembly of haplotypes Categ... -
NonChimericOriginalAlignmentReadFilter
Filters reads whose original alignment was chimeric. Category ... -
NonNFastaSize (Picard)
Counts the number of non-N bases in a fasta file.This tool takes any FA... -
NonZeroFragmentLengthReadFilter
Filter out reads with fragment length different from zero Category ... -
NonZeroReferenceLengthAlignmentReadFilter
Filter out reads that do not align to the reference Category R... -
NormalizeFasta (Picard)
Normalizes lines of sequence in a FASTA file to be of the same length.T... -
NotDuplicateReadFilter
Filter out reads marked as duplicate Category Read Filters ... -
NotSecondaryAlignmentReadFilter
Filter out reads representing secondary alignments Category Re... -
NotSupplementaryAlignmentReadFilter
Filter out reads representing supplementary alignments Category ... -
OrientationBiasReadCounts
Count of read pairs in the F1R2 and F2R1 configurations supporting REF ... -
OriginalAlignment
Number of alt reads with an OA tag that doesn't match the current align... -
OverclippedReadFilter
Filter out reads that are over-soft-clipped Category Read Filt... -
OxoGReadCounts
Count of read pairs in the F1R2 and F2R1 configurations supporting REF ... -
PairedReadFilter
Filter out unpaired reads Category Read Filters Overv... -
ParallelCopyGCSDirectoryIntoHDFSSpark (BETA)
Parallel copy a file or directory from Google Cloud Storage into the HD... -
PassesVendorQualityCheckReadFilter
Filter out reads failing platfor/vendor quality checks Category ... -
PathSeqBuildKmers
Builds set of host reference k-mers Category Metagenomics ... -
PathSeqBuildReferenceTaxonomy
Builds a taxonomy datafile of the microbe reference Category M... -
PathSeqBwaSpark
Step 2: Aligns reads to the microbe reference Category Metagen... -
PathSeqFilterSpark
Step 1: Filters low quality, low complexity, duplicate, and host reads ... -
PathSeqPipelineSpark
Combined tool that performs all steps: read filtering, microbe referenc... -
PathSeqScoreSpark
Step 3: Classifies pathogen-aligned reads and generates abundance score... -
Pileup
Prints read alignments in samtools pileup format Category Cove...