daisyyr

Hi, everyone~ Is this problem solved now? It seems that I've encounted similiar problems. I'm using GATK4.2 and hg38 data. 11:43:25.661 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript...

Thanks for your answer! It's really useful. I've encountered the same problem. BTW, where can I find the source code for germinate() function ? I could not find it under...

> GATK BaseRecalibration is almost certainly the issue. Most of our tools are written to use Illumina standard quality scores, BaseRecalibration will push the quality scores well outside the expected...

> It seems the BWA_WT: path is different from the one provided in in vars file: 'n' => 'myworkpath/Project/Project_NB_4s/basic_analysis/no_recal_bam/T1609B_clean_dedup.bam', 'nidx' => 'myworkpath/Project/Project_tumor/basic_analysis/no_recal_bam/T1609B_clean_dedup.bai', > > BAM_WT : myworkpath/Project/Project_tumor/basic_analysis/no_recal_bam/T1609B_clean_dedup.bam > > Commands...