Joseph Thorpe
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Activity overview
Latest activity by Joseph Thorpe-
Joseph Thorpe commented,
Thank very much this worked
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Joseph Thorpe commented,
Just to add, changing the mapping quality for that read to be above 20 then HC will call the variant, so the paramaters --disable-read-filter doesnt seem to do anything. In the original post I didn...
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Joseph Thorpe created a post,
GATK haplotype caller struggling to find variant that exists
Hi, I have been trying to call variants on my bam file on a specific region becuase I was missing some variants that were to be expected when calling other parts of the genome. I have been trying t...
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Joseph Thorpe created a post,
GenotypeGVCF not getting all samples
REQUIRED for all errors and issues: a) GATK version used: v4.1.4.1b) Exact command used: First genomicsDB:gatk --java-options "-Xmx24g -Xms24g" GenomicsDBImport --genomicsdb-workspace...