4.0.6.0
Tool documentation for GATK release 4.0.6.0
-
IntervalListToBed (Picard)
Converts an Picard IntervalList file to a BED file. Categor... -
IntervalListTools (Picard)
A tool for performing various IntervalList manipulations Summar... -
IntervalOverlapReadFilter
Filters out reads that don't overlap the specified region. NOTE... -
LeftAlignAndTrimVariants
Left align and trim vairants Category Variant Manipula... -
LeftAlignIndels
Left-aligns indels from reads in a SAM/BAM/CRAM file Catego... -
LibraryReadFilter
Keep only reads from the specified library Category Re... -
LiftOverIntervalList (Picard)
Lifts over an interval list from one reference build to another... -
LiftoverVcf (Picard)
Lifts over a VCF file from one reference build to another. Sum... -
LikelihoodRankSumTest
Rank sum test of per-read likelihoods of REF versus ALT reads (... -
MakeSitesOnlyVcf (Picard)
This tool reads a VCF/VCF.gz/BCF and removes all genotype infor... -
MappedReadFilter
Filter out unmapped reads Category Read Filters ... -
MappingQuality
Median mapping quality of reads supporting each allele (MMQ) ... -
MappingQualityAvailableReadFilter
Filter out reads without available mapping quality Category... -
MappingQualityNotZeroReadFilter
Filter out reads with mapping quality equal to zero Categor... -
MappingQualityRankSumTest
Rank sum test for mapping qualities of REF versus ALT reads (MQ... -
MappingQualityReadFilter
Keep only reads with mapping qualities within a specified range... -
MappingQualityZero
Count of all reads with MAPQ = 0 across all samples (MQ0) C... -
MarkDuplicates (Picard)
Identifies duplicate reads. This tool locates and tags duplica... -
MarkDuplicatesGATK (EXPERIMENTAL)
Examines aligned records in the supplied SAM/BAM/CRAM file to l... -
MarkDuplicatesSpark (BETA)
MarkDuplicates on Spark Category Read Data Manipulatio... -
MarkDuplicatesWithMateCigar (Picard)
Identifies duplicate reads, accounting for mate CIGAR. This to... -
MarkIlluminaAdapters (Picard)
Reads a SAM or BAM file and rewrites it with new adapter-trimmi... -
MatchingBasesAndQualsReadFilter
Filter out reads where the bases and qualities do not match ... -
MateDifferentStrandReadFilter
Keep only reads with mates mapped on the different strand C... -
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... -
MergeSamFiles (Picard)
Merges multiple SAM and/or BAM files into a single file. This ...