1. Community
2. Germline

Hi  I observed an inconsistency between these 2 files generated for 2 samples in 2 different runs of GCNV workflow using GATK 4.2.6.1 docker image. I am not sure if my problem is similar to this on...

• SkyWarrior
• July 30, 2022 16:32
• 3 followers
• 12 comments
• 0 votes

1. Community
2. Other

Hi  I just tried 4.2.6.0 docker image for germline CNV workflow and came across this error message in the logs.  08:57:35.253 DEBUG ScriptExecutor -   --contig_ploidy_prior_table=/home/GATK_CNV/con...

• SkyWarrior
• April 10, 2022 09:02
• Edited
• 2 followers
• 1 comment
• 0 votes

1. Community
2. General Discussion

Hi I would like to share an experience and ask a few questions regarding gCNV steps especially GermlineCNVCaller.  I use different systems for gCNV workflows and I observe massive difference betwee...

• SkyWarrior
• January 25, 2022 13:29
• 2 followers
• 8 comments
• 0 votes

1. Community
2. Other

Hi I have a question regarding the definition given in the SplitNCigarReads tool.  This tool should generate K+1 reads where K is the number of N Cigars in the mapped read for RNAseq data. However ...

• SkyWarrior
• June 21, 2021 13:29
• Edited
• 3 followers
• 9 comments
• 0 votes

1. Community
2. Other

I am observing a strange behavior with GermlineCNVCaller which used to work fine before but now acting strange on different computers. Previously I performed a CNV calling on 11 WGS samples using d...

• SkyWarrior
• December 02, 2020 05:52
• Edited
• 4 followers
• 8 comments
• 0 votes

1. Community
2. Germline

Hi  I would like to share a new finding of mine where I was blindsided by the default parameters of gatk FilterIntervals during a whole genome CNV calling.  The story began with a trio where I dete...

• SkyWarrior
• August 04, 2020 21:30
• Edited
• 4 followers
• 4 comments
• 0 votes

1. Community
2. Germline

I have received the below error when I tried working with GermlineCNV workflow in cohort mode.   /home/exome/miniconda3/envs/gatk/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Con...

• SkyWarrior
• February 06, 2020 10:25
• Edited
• 3 followers
• 5 comments
• 0 votes

1. Community
2. Other

Hi When gatk python environment is installed to a fresh installation I am getting an error regarding missing dependencies however it is not stated anywhere during installation.   18:51:11.774 DEBUG...

• SkyWarrior
• February 06, 2020 07:21
• Edited
• 5 followers
• 17 comments
• 1 vote