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jfarrell

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Latest activity by jfarrell
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    jfarrell commented,

    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 o...

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    jfarrell commented,

    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...

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    jfarrell commented,

    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...

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    jfarrell commented,

    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...

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    jfarrell commented,

    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...

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    jfarrell commented,

    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...

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    jfarrell created a post,

    What is the Dragen filtering rule based on QUAL?

    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...

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    jfarrell commented,

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