Avatar

GATK Team

  • Total activity 8242
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 1 user
  • Votes 0
  • Subscriptions 0

Activity overview

Latest activity by GATK Team
  • Avatar

    GATK Team created an article,

    (How to) Map and clean up short read sequence data efficiently

    (How to) Map and clean up short read sequence data efficiently In this tutorial, you will learn to emulate the methods used by the Broad Genomics Platform to pre-process your short read sequenci...

  • Avatar

    GATK Team created an article,

    I am unable to use VQSR (recalibration) to filter variants

    This document was written for GATK3. Some commands or information may be out of date or incorrect. We are in the process of updating documentation to reflect changes in GATK4. If you have questions...

  • Avatar

    GATK Team created an article,

    (How to) Map reads to a reference with alternate contigs like GRCH38

    This document was written for GATK3. Some commands or information may be out of date or incorrect. We are in the process of updating documentation to reflect changes in GATK4. If you have questions...

  • Avatar

    GATK Team created an article,

    (How to) Fix a badly formatted BAM

    This document was written for GATK3. Some commands or information may be out of date or incorrect. We are in the process of updating documentation to reflect changes in GATK4. If you have questions...

  • Avatar

    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 ...

  • Avatar

    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...

  • Avatar

    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...

  • Avatar

    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...

  • Avatar

    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...

  • Avatar

    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 ...