
suzy_bunters
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Recent activity by suzy_bunters Sort by recent activity-
A USER ERROR has occurred: Badly formed genome unclippedLoc
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.0.10.1 b) Exact command used: gatk --java-options "-Xmx4G -XX:+UseParallelGC -XX:ParallelGCThreads=2" HaplotypeCalle...
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emit-ref-confidence error using single sample BAM
Answereda) GATK version used: 4.1.7.0 b) Exact command used: gatk HaplotypeCaller -R final.fasta -I ${sampleName}_markdup.bam -O /${sampleName}.g.vcf.gz -ERC GVCF c) Entire error log: A USER ERROR has occu...
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HaplotypeCaller - incompatible contigs (one scaffold only)
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.7.0b) Exact command used: gatk HaplotypeCaller -R final.fasta -I ${sampleName}_markdup.bam -O /${sampleName}.g.vcf....