Morgan Sparks
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Recent activity by Morgan Sparks Sort by recent activity-
GATK Handling of Paralogs
I work on an organism that is highly paralogous (salmon). It generally functions as a diploid with occasional tetraploidy and numerous paralogs. I am trying to understand how GATK--particularly the...
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GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source:
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk-4.2.2.0 b) Exact command used: while read -a linedo/home/sparks35/gatk-4.2.2.0/gatk --java-options "-Xmx36g -Xms36g...
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markduplicatesSpark .bam.parts output error (directory already exists)
AnsweredJust to preface, I downloaded gatk into my remote cluster home directory because using the version hosted in our bioinformatic applications directory (v. GATK/4.2.2.0) was failing at setting up the...