Le Qi
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discrepency between CollectReadCounts and CollectWgsMetrics
REQUIRED for all errors and issues: a) GATK version used: v4.5.0.0b) Exact command used: For CollectWgsMetrics: Java -jar picard.jar CollectWgsMetrics I=input.bam O=output.txt R=hg38.fasta For Co...
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Pooling reads from NovaSeq 6000 and NovaSeq X plus
Hi, I have about 20X coverage-worth of reads from NovaSeq 6000, and I need to sequence them deeper to get 30X. I'm facing the choice of using the NovaSeq 6000 to keep it consistent or using the new...
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DRAGEN-GATK and joint genotyping
I have a general question about the new DRAGEN-GATK pipeline and how it interacts with joint genotyping step. I understand that the DRAGEN-GATK is currently supporting only single sample mode, and ...
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Error import gcnvkernel during GATK-SV cohort mode on local HPC
REQUIRED for all errors and issues: I understand that the GATK-SV cromwell pipeline is meant for Terra, but I'm trying to implement it on local HPCs. I'm at the trainGCNV step and there's an error ...