Yangyxt
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JointGermlineCNVSegmentation
AnsweredREQUIRED for all errors and issues: a) GATK version used: 4.2.5.0b) Exact command used: NAc) Entire program log:NA Why there isnt a manual for JointGermlineCNVSegmentation this tool ? I saw this to...
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run into PythonScriptExecutorException when executing PostprocessGermlineCNVCalls about positional arguments
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.2.0b) Exact command used: ${gatk} PostprocessGermlineCNVCalls \ --model-shard-path ${gCNV_model_prefix}-model \ --c...
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VQSR RscriptExecutorError (fail reading tranches table)
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.9.0 b) Exact command used: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true ...
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Detect other jobs writing to GenomicDB with GenomicDBImport
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How ...
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VQSR positive training model failed to converge
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1b) Exact command used: ## SNP mode time$gatk VariantRecalibrator -AS \ -R $ref_gen/ucsc.hg19.fasta \ -V ${vcf} \...
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Import GVCFs using GenomicsDBImport one chromosome at a time and parallel the jobs encounter a Duplicate Sample Name Error
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1b) Exact command used: time ${gatk} --java-options "-Xmx8g -Xms2g" GenomicsDBImport \--tmp-dir /paedwy/disk1/yang...
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Combine GVCF generate java.lang.NullPointerException
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1 b) Exact command used: time "$gatk" CombineGVCFs \-G StandardAnnotation \-G AS_StandardAnnotation \-R "$ref_gen...
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HaplotypeCaller--Exception in thread "main" java.lang.OutOfMemoryError: Java Heap Size. Allele -Specific- Annotation
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.4.1b) Exact command used: gatk --java-options "-Xmx60G" HaplotypeCaller \--emit-ref-confidence GVCF \-R $ref_gen/ucs...
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HaplotypeCaller--Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How do I (....
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MarkDuplicatesSpark consumes enormous amount of RAM
AnsweredDear Officer, Thank you for bringing MarkDuplicatesSpark here. I've been using it to deal with targeted sequencing data. It works fine until the last run, in which I use it on a 2-3 times bigger ba...