GATK Team
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Activity overview
Latest activity by GATK Team-
GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
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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GATK Team created an article,
CalibrateDragstrModel
estimates the parameters for the DRAGstr model Category Short Variant Discovery Overview Estimates the parameters for the DRAGstr model for an input sample. ...