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Thank you bhanuGandham! 1. I tried to use the gatkcondaenv.yml from GitHub for installation with conda but it failed with the attached message. 2. I previously installed gatk4 into my conda environment with "conda install gatk4" and every othe…
Content of stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/mnt/operation/RedCellNGS/Processed_bam_vcf_1/bam/cromwell-executions/CNN_filtering/982a2730-51ee-4e06-aa2a-6f8e9ab0ab3d/call-CNNScoreVariants/shard-0/tmp.0bdad571 03:16:40.188 INFO N…
That's a very good suggestion, I shall try it out. Thank you!
Thank you SkyWarrior! I will do do joint genotyping then. Is it true that VQSR cannot be applied in my scenario and I can only perform hard filtering? Thank you once again!