Avatar

GATK Team

  • Total activity 15271
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 13 users
  • Votes 0
  • Subscriptions 0

Articles

Votes on activity by GATK Team Sort by votes Recent activity Votes
  • * 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...

  • BaseRecalibrator

    Generates recalibration table for Base Quality Score Recalibration (BQSR) Category Read Data Manipulation Overview First pass of the base quality score recalibration. Gen...

  • 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...

  • 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...

  • 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...

  • MappedReadFilter

    Filter out unmapped reads Category Read Filters Overview Filter out unmapped reads. Unmapped reads are defined by three criteria: SAM flag value 0x4 ...

  • 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...

  • InsertSizeMetrics

    Metrics Category Metrics Overview Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually ...

  • 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...

  • 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...