GATK Team
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Recent activity by GATK Team Sort by recent activity-
CleanSam (Picard)
Cleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads Category Read Data Manipulation Overview @au...
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CheckTerminatorBlock (Picard)
Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise Category Diagnostics and Quality Control Overview Simple class to check th...
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ReadLengthReadFilter
Keep only reads whose length is within a certain range Category Read Filters Overview Keep only reads whose length is ≥ min value and ≤ max value. ReadLength...
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QualityYieldMetrics
Back to Tool Docs Index Metrics Category Metrics Overview A set of metrics used to describe the general quality of a BAM file This table summa...
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HmerMotifs
Right Motif Flow Annotation Category Flow Annotations Overview Flow Annotation: motifs to the left and right of the indel Return to top ...
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GtcToVcf (Picard)
GtcToVcf takes an Illumina GTC file and converts it to a VCF file using several supporting files. A GTC file is an Illumina-specific file containing called genotypes in AA/AB/BB forma...
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CheckPileup
Compare GATK's internal pileup to a reference Samtools mpileup Category Diagnostics and Quality Control Overview Compare GATK's internal pileup to a reference Samt...
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CreateSomaticPanelOfNormals (BETA)
Make a panel of normals for use with Mutect2 Category Variant Filtering Overview Create a panel of normals (PoN) containing germline and artifactual sites for use ...
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FilterVariantTranches
Apply tranche filtering Category Variant Filtering Overview Apply tranche filtering to VCF based on scores from an annotation in the INFO field. The annotation ca...
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CallableLoci (EXPERIMENTAL)
Determine callable status of loci Category Coverage Analysis Overview Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome ...