Cher Wei Yuan
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Activity overview
Latest activity by Cher Wei Yuan-
Cher Wei Yuan commented,
Dear Genevieve I tried several parameters (Xmx4/12/20G + 48 threads, Xmx100G + 1/4/24 threads, Xmx200G + 48 threads) but the furthest I got was still task 53.0 in stage 0.0 (TID 53), where it runs...
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Cher Wei Yuan commented,
Dear Genevieve I tried using 1, 4 and 12 threads but the program runs indefinitely still. May I seek your help in troubleshooting? Here is the printout from using 4 threads: gatk FindBadGenomicKme...
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Cher Wei Yuan created a post,
FindBadGenomicKmersSpark running indefinitely
AnsweredDear GATK staff May I seek your help in troubleshooting FindBadGenomicGenomicKmersSpark? I wish to use it to generate a list of ubiquitous kmers to ignore for StructuralVariationDiscoveryPipelineSp...
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Cher Wei Yuan commented,
Hello Genevieve Brandt (she/her) I did not realized my HaplotypeCaller parameters output a gvcf. I removed "-ERC BP_RESOLUTION \-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB ...
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Cher Wei Yuan commented,
Hi GenevieveThank you so much. Here are two lines with variance: chr7 96317809 . TA T,<NON_REF> 798.04 . BaseQRankSum=0.929;CNN_2D=-10.974;DP=189;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRank...
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Cher Wei Yuan created a post,
FilterVariantTranches Error: 'no variants with INFO score key "CNN_2D"'
AnsweredHello GATK staff and community I have encountered an issue while working with FilterVariantTranches as it does not detect the INFO score key "CNN_2D" in the input vcf. Please see below for more det...