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GATK Team

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Latest activity by GATK Team
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    GATK Team created an article,

    When HaplotypeCaller and Mutect2 do not call an expected variant

    You may find, after running an analysis with HaplotypeCaller or Mutect2, that your results do not show a variant that you were expecting to find. This is because the default assembly/calling option...

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    GATK Team created an article,

    When HaplotypeCaller or Mutect2 do not call an expected variant

    You may find, after running an analysis with HaplotypeCaller or Mutect2, that your results do not show a variant that you were expecting to find. This is because the default assembly/calling option...

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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,

    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,

    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 ...

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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,

    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...