Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
GATK4: Trouble running "GATK 4 CNV Proportional Coverage for Capture"
I am trying to run "GATK 4 CNV Proportional Coverage for Capture" on
samples with no matched normals sequenced using TSCA (TrueSeq Custom
I understand that the first step is to run "GATK 4 CNV Proportional
Coverage for Capture" and configure the task replacing
gatk4cnv_padded_target_bed_capture with the bed file with the intervals
I am getting the attached error and stdout. It seems that it doesn't like
the fact that some intervals are overlapping. What is the workaround to
I am running GATK4 workflow because I would like to run absolute to
estimate the purity of the samples. If there is a simpler way to get the
purity of such samples, please let me know.