Yangyxt
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Activity overview
Latest activity by Yangyxt-
Yangyxt commented,
Hi, I've ran into this issue recently. Basically, I'm using 43 samples (we only have 43 WES samples captured with the same set of probe) to run DetermineGermlineContigPloidy in COHORT mode. Severa...
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Yangyxt created a post,
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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Yangyxt commented,
Hi Geraldine Van der Auwera, I wonder, since the new added mode of dragen-mode for HC(which should be used on dragmap generated BAM files I suppose), can we mix the GVCFs generated by the old, trad...
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Yangyxt commented,
Hi Jonathan Klonowski, Actually you can use GNU parallel to wrap the GenomicdDBImport for parallel running.
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Yangyxt created a post,
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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Yangyxt commented,
I can provide VCF to you if needed.
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Yangyxt commented,
I use GATK 4.1.9.0 and seems the issue happened again. Although I'm not using HC, instead I used LeftAlignAndTrimVariants. Here is the error log: htsjdk.tribble.TribbleException: Badly formed v...
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Yangyxt created a post,
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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Yangyxt commented,
Dear Brandt, It just occurred to me that the meta-lines might change in gvcf files using different version of GATK. Since it is a vidmapper exception, I checked the vidmap.json in genomicDB repo a...
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Yangyxt commented,
Dear Brandt, I just ran into the same issue here and I used GATK 4.1.9.0(However, the genomicDB I generated was from GATK 4.1.8.1). the link of github issue report seems to be relevant with conflic...