simon lee
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Activity overview
Latest activity by simon lee-
simon lee commented,
I should just add one more thing: When running in non-parellel mode, or when running the first or even the second job on the hpc, I do not get this error. the module load executes without a problem...
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simon lee created a post,
improt gcnvkernel fails. somehting to do with theano lock
AnsweredREQUIRED for all errors and issues: a) GATK version used:gatk/4.1.4.1-gcccore-8.3.0-java-11 b) Exact command used: gatk GermlineCNVCaller \--run-mode COHORT \-L $intervals \--contig-ploidy-calls $...
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simon lee created a post,
CollectReadCounts tutorial incorrectly states default read quality threshold
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.4.1b) Exact command used: gatk CollectReadCounts \--minimum-mapping-quality $MQmin \-L $binnedIntervalsPadded \-R $...
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simon lee commented,
Edit: earlier I said GL, when I meant to say PL. PL is the genotype likelihood in phred scale, not GL. Hope that clears up any confusion.
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simon lee commented,
PROBLEM SOLVED: (I solved the problem by deleting GP, rather than fixing it) The issue all along as been with the number of fields in GP, but also in PRI, which I assume is the prior probabilities ...
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simon lee commented,
Hi Pamela, I have an update. Forgive me if the following information is trivial. I am still learning and I have just gone through confirming the following: I have concluded the exact nature of th...
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simon lee commented,
Hey Pamela, I wanted to add a couple extra notes regarding the error with the GP variable (Bayes posterior phenotype probability). I have run bcftools view -r to remove the region with the "wrong n...
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simon lee commented,
So there are two errors occuring. One at chr22:10515074, the other at chr22:10513871. (occuring first in the error log) at chr22:10515074, the error is: Error at chr22:10515074, the tag GP has wron...
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simon lee created a post,
error: tag GP has wrong number of fields. running bcftools norm -m-any
If you are seeing an error, please provide(REQUIRED) : GATK version: 4.1.4.1Bcftools version: 1.10.2 (gatk) n11137185@cl5n016:~> inputPrefix=/home/n11137185/04_tiwiAssembly/gvcfEnv/gvcfSamplesCombi...