WangZiwei
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Activity overview
Latest activity by WangZiwei-
WangZiwei commented,
Hello Genevieve Brandt (she/her) perhaps Mills_and_1000G_gold_standard.indels.hg38.vcf.gz(.tbi) caused the problem, because when I redownloaded it from GATK resource bundle, the error just dissape...
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WangZiwei created a post,
java.lang.OutOfMemoryError using BaseRecalibrator
AnsweredUpdate The error has been solved by redownloading Mills_and_1000G_gold_standard.indels.hg38.vcf.gz(.tbi) but the error message is distracting anyway. -----------------------------------------------...
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WangZiwei commented,
https://gatkforums.broadinstitute.org/dsde/discussion/11193/funcotator-information-and-tutorial doesn't exist
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WangZiwei commented,
Hi David Benjamin Could you please help explain the filteringStats.tsv file, the output of 'FilterMutectCalls' tool? Or is there something like a detailed description of this output? Currently I h...
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WangZiwei created a post,
Is it better to 'CollectAllelicCounts' using bam files local assembled by Haplotypecaller or Mutect2?
Answered(REQUIRED) Please provide: a) GATK version used: 4.1.8.0b) Exact command used: example code in https://gatk.broadinstitute.org/hc/en-us/articles/360035890011 gatk --java-options "-Xmx3g" CollectAl...
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WangZiwei commented,
Hi Jason Cerrato My reply seems to be pending approval. I wonder if you could see it. Regards. Wang Ziwei
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WangZiwei commented,
Hi Jason Cerrato I found these 2 files have no intersection. I think it is because I generate variants_for_contamination.vcf in a wrong way. so I add -L xgen_exome_panel_v2_targets_b37_somatic.int...
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WangZiwei commented,
Hi Jason Cerrato , I switched to gatk 4.1.4.1 docker but still got an error at "GetPileupSummaries" step and exit, I believe it is involved in detecting variants for contamination things. Here is t...
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WangZiwei commented,
Hi Jason Cerrato Sorry for replying late. I did arbitarily change the gatk4 version to 4.1.8.0, I will keep the workflow as it is and try to run it again. The workflow I used is the one archived i...
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WangZiwei commented,
Hi Jason Cerrato this post was pended before and I have post another one here: https://gatk.broadinstitute.org/hc/en-us/community/posts/360071756371-Mutect2-PoN-best-practice-pipeline-failed-with-...