Le Qi
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Activity overview
Latest activity by Le Qi-
Le Qi commented,
Hi Gökalp Çelik, I'm trying to produce gVCF files using the wdl pipeline suggested here https://github.com/broadinstitute/gatk/tree/master/scripts/mitochondria_m2_wdl There is no problem producing...
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Le Qi commented,
Hi Gökalp Çelik Thanks for the reply. I understand this is how CollectReadCounts works, so it's intended behavior then. The only reason I called it coverage was that it's the first step to generate...
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Le Qi created a post,
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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Le Qi commented,
Thank you Gökalp Çelik!
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Le Qi created a post,
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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Le Qi commented,
Hi Ricky Magner Thanks for your reply! I was specifically talking about the genotypeGVCFs tool from GATK. I could run the DRAGEN-GATK output gVCF through genotypeGVCFs without problems. I'm curious...
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Le Qi created a post,
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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Le Qi commented,
Hi Gökalp Çelik The workflow works fine on Terra and on my own MacOS with docker, which is not allowed on our HPC. I think the problem is with singularity somehow. I managed to get around the probl...
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Le Qi commented,
Hi Gökalp Çelik I managed to activate gatk conda environment and set THEANO_FLAGS environmental variable, but import gcnvkernel still showed the same error. I've successfully adopted the previous 2...
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Le Qi commented,
Hi Gökalp Çelik I tried the new environmental variable. I have the same errors and I can see the cache files generated in the specified path when I just try to import gcnvkernel. I had similar cach...