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GATK Team

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Latest activity by GATK Team
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    GATK Team created an article,

    Mitochondrial short variant discovery (SNVs + Indels)

    Purpose The mitochondrial genome poses several challenges to the identification and understanding of somatic variants. The circularity of the mitochondrial genome means that the breakpoint in the ...

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    GATK Team created an article,

    (How to) Generate an unmapped BAM from FASTQ or aligned BAM

    Objective Here we outline how to generate an unmapped BAM (uBAM) from either a FASTQ or aligned BAM file. We use Picard's FastqToSam to convert a FASTQ (Option A) or Picard's RevertSam to convert ...

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    GATK Team created an article,

    Which training sets arguments should I use for running VQSR?

    This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based...

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    GATK Team created an article,

    Running GATK on the cloud (Overview)

    There are many ways to run GATK for your analyses, and the best option for you depending on what infrastructures you are most comfortable working with. Terra, the user-friendly choice Our first ...

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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,

    CleanSam (Picard)

    Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads Category Read Data Manipulation Overview ...

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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,

    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,

    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 ...