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* Tool Documentation Index
Copy Number Variant Discovery Tools that analyze read coverage to detect copy number variants. Name Summary AnnotateIntervals Annotates intervals with GC content, mappability, and se...
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BaseRecalibrator
Generates recalibration table for Base Quality Score Recalibration (BQSR) Category Read Data Manipulation Overview First pass of the base quality score recalibration. Gen...
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PossibleDeNovo
Existence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo) Category Variant Annotations Overview Existence of a de novo mut...
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MergeVcfs (Picard)
Combines multiple variant files into a single variant file.Inputs One or more input file in VCF format (can be gzipped, i.e. ending in ".vcf.gz", or binary compressed, i.e. endin...
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NonZeroReferenceLengthAlignmentReadFilter
Filter out reads that do not align to the reference Category Read Filters Overview Filter out reads that do not align to the reference. Filter interprets each of t...
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MappedReadFilter
Filter out unmapped reads Category Read Filters Overview Filter out unmapped reads. Unmapped reads are defined by three criteria: SAM flag value 0x4 ...
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TransferReadTags (EXPERIMENTAL)
Incorporate read tags in a SAM file to that of a matching SAM file Category Read Data Manipulation Overview This tool takes a pair of SAM files sharing the same re...
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InsertSizeMetrics
Metrics Category Metrics Overview Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually ...
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ASEReadCounter
Generates table of filtered base counts at het sites for allele specific expression Category Coverage Analysis Overview Calculate read counts per allele for allele...
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UmiAwareMarkDuplicatesWithMateCigar (Picard) (EXPERIMENTAL)
Identifies duplicate reads using information from read positions and UMIs. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads aredefined as origina...