4.2.4.0
Tool documentation for GATK release 4.2.4.0
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MateDifferentStrandReadFilter
Keep only reads with mates mapped on the different strand C... -
MateDistantReadFilter
Keep only paired reads with mates mapped >= mate-too-distant-le... -
MateOnSameContigOrNoMappedMateReadFilter
Keep only reads whose mate maps to the same contig or is unmapp... -
MateUnmappedAndUnmappedReadFilter
Filters reads whose mate is unmapped as well as unmapped reads.... -
MeanQualityByCycle (Picard)
Collect mean quality by cycle.This tool generates a data table ... -
MeanQualityByCycleSpark (BETA)
MeanQualityByCycle on Spark Category Diagnostics and Q... -
MergeBamAlignment (Picard)
Merge alignment data from a SAM or BAM with data in an unmapped... -
MergePedIntoVcf (Picard)
MergePedIntoVcf takes a single-sample ped file output from zCal... -
MergeSamFiles (Picard)
Merges multiple SAM and/or BAM files into a single file. This ... -
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
Models segmented copy ratios from denoised copy ratios 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... -
NotProperlyPairedReadFilter
Keep only paired reads that are not properly paired Categor... -
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... -
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...