Yangyxt
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Dear Bhanu Gandham Thanks for the reply, I took a look at the arguments in the doc's page. I found that the value of --spark-master is URL str. In my case, I ran MarkDuplicatesSpark on my instituti...
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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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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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Hi Jonathan Klonowski, Actually you can use GNU parallel to wrap the GenomicdDBImport for parallel running.
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I can provide VCF to you if needed.
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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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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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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...
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Dear Brandt, I ran into the same issue and then trying to use SortVcf to sort every input before using GatherVcfs to concat them. Then I hit this error ( I added the java option -DGATK_STACKTRACE_O...
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I also tried : gatk SelectVariants \ -R reference.fasta \ -V variants.vcf \ -select "vc.getGenotype('<sampleID>').isHet()" \ -O output.vcf Which failed either. BTW, I'm trying on GA...