Avatar

jfarrell

Follow
  • Total activity 14
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 5

Activity overview

Latest activity by jfarrell
  • Avatar

    jfarrell commented,

    1. Getting Started
    2. Tutorials
    3. (How to) Call rare germline copy number variants

    This link below is broken  from above.  Has there been an update with the Tutorial which matches the latest WDL pipeline? ftp://ftp.broadinstitute.org/tutorials/dataset   Download tutorial_11684.ta...

  • Avatar

    jfarrell commented,

    1. Community
    2. Non-Human
    3. Speeding up GenotypeGVCFS? GATK4

    kvn95ss and Genevieve-Brandt-she-her Regarding the bypass-feature reader recommendation, the documentation mentions the VCFs must be normalized.  Are reblocked gvcfs normalized and ready to use or ...

  • Avatar

    jfarrell commented,

    1. Tool Index
    2. 4.2.6.1
    3. GenomicsDBImport

    To use the --bypass-feature-reader option for GenomicsDBImport, the documentation  indicates the VCF must be normalized, block compressed and indexed.    Use htslib to read input VCFs instead of GA...

  • Avatar

    jfarrell commented,

    1. Community
    2. Non-Human
    3. Speeding up GenotypeGVCFS? GATK4

    This is a potential solution that I will be testing out with my next batch of crams. There is now support in the 4.2.6.1 CombineGVCFs and GenotypeGVCFs for "reblocked" GVCFs as produced by the Rebl...

  • Avatar

    jfarrell commented,

    1. Community
    2. Non-Human
    3. Speeding up GenotypeGVCFS? GATK4

    It runs to completion  if I  give the job a lot of memory (80 -120 gb)  and target a small interval for the genomicsDB with  2000 samples for each chromosome.  The output vcf.gz is only 55M for onl...

  • Avatar

    jfarrell commented,

    1. Community
    2. Non-Human
    3. Speeding up GenotypeGVCFS? GATK4

    These are useful suggestions on speeding up GenotypwGVCFs which I am using.  None of them address the large amount of memory used no matter how small the target size that is specified.  GenotypeGVC...

  • Avatar

    jfarrell commented,

    1. Community
    2. Non-Human
    3. Speeding up GenotypeGVCFS? GATK4

    Based on some  runs with GATK 4.2.0.0, it does seem to use a lot of memory no matter the size of the interval and it correlates with the size of the chromosome.   The memory used increases as the c...

  • Avatar

    jfarrell created a post,

    What is the Dragen filtering rule based on QUAL?

    1. Community
    2. Germline

    How do I filter variants produced by the GATK DRAGEN model? It was stated in the GATK 4.2 blog announcement that the DRAGEN has a very simple hard-filtering rule based on the QUAL score only.  What...

    • jfarrell
    • 2 followers
    • 1 comment
    • 0 votes
  • Avatar

    jfarrell commented,

    1. Tool Index
    2. 4.2.0.0
    3. CalibrateDragstrModel (BETA)

    Where is the documentation for the ComposeSTRTableFile tool referenced in this article?  Don't see it in the Tools Documentation.