NawarDalila
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Activity overview
Latest activity by NawarDalila-
NawarDalila created a post,
What is the difference between the segmented vcf file and .call.seg file
Hi, I am following this guide to call our CNV calls https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants The results are presen...
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NawarDalila created a post,
PostprocessGermlineCNVCalls generate a segment file with missing GT field for the segment file
Hi, I am running the CNV workflow as recommended from this source: https://github.com/broadinstitute/gatk/blob/master/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl I am using GATK v4.2....
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NawarDalila created a post,
ScatterIntervalList error message when running DRAGEN-GATK on HPC
AnsweredHi, I am running DRAGEN-GATK pipeline on our HPC and the workflow stopped at some point with this error: [2022-01-14 13:51:27,76] [info] WorkflowManagerActor: Workflow c48ca756-d705-4a0a-a45f-b6aa...
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NawarDalila created a post,
bait_set_name in WGS DRAGEN-GATK pipeline
AnsweredHi, I am running the DRAGEN-GATK pipeline on our HPC and it is failing with this error: Failed to evaluate input 'references' (reason 1 of 1): Error(s):No value for field 'evaluation_interval_list...
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NawarDalila created a post,
Missing files in GATK resource bundle hg38
AnsweredDear all, I am trying to run your WGS analysis pipeline DRAGEN-GATK. I am faced with two missing files in your resource bundle that are supplied by your pipeline input files. Those two files are: ...
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NawarDalila commented,
Hi, I can't seem to find the str file, would you please check the resource bundle? Thanks I used this link to search: gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.str
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NawarDalila commented,
Dear all, Where can I find the WDL and JSON files for DRAGEN-GATK Germline analysis v1 to be used on an HPC? Thanks for your help Nawar
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NawarDalila created a post,
How do I call a variant even if its region is not considered active by HaplotypeCaller?
I have a sample (Sample1) that is analyzed using BWA v0.7.6a-r433 and GATK 4.1.0.0. I called the variants using HaplotypeCaller using the ERC mode (GVCF) and then joint genotyped the samples (8 sam...
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NawarDalila commented,
Hi, I have kind of the same issue. Here is what I experienced lately and I really can't figure out a starting point. I have a sample (Sample1) that is analyzed using BWA v0.7.6a-r433 and GATK 4.1.0...
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NawarDalila commented,
Chase He yes this is right.