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GATK Team

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Activity overview

Latest activity by GATK Team
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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...

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    GATK Team created an article,

    PrintReadsSpark

    PrintReads on Spark Category Read Data Manipulation Overview Additional Information Read filters This Read Filter is automatically applied...

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    GATK Team created an article,

    CountBasesSpark

    Counts bases in the input SAM/BAM Category Coverage Analysis Overview Calculate the overall number of bases SAM/BAM/CRAM file Input A single BAM file ...