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We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
MINIMUM_GENOME_FRACTION - doesn't impact results on picard.jar CollectGcBiasMetrics
JonR
IndianaMember ✭
I ran picard CollectGCBiasMetrics on 3 different bamfiles using 10 different settings creating a total of 30 plots. I found no difference between any of the results.
MINIMUM_GENOME_FRACTION was set
from 1.0E-1 to 1.0E-5 (default)
and
from .1 to .00001
Log files are attached. Any idea what's going on or how to get this variable to stick? Thank you in advance for the feedback
Tagged:
Answers
@JonR
Hi,
Which version of the tool are you using? Can you post some example plots that show no difference?
Thanks,
Sheila
Here you go. Same dataset, 2 different notations, 2 different settings each notation. MG is minimum genome fraction. Log files attached to previous post. This is 900,000 reads of Ecoli aligned with BWA mem
@JonR
Hi,
Alright, can you try with the very latest version of Picard. There is a new release that I am hoping will have a fix for this. If not, I will put a bug report in.
Thanks,
Sheila
Hi,
How to understand the option 'MINIMUM_GENOME_FRACTION' ? In the manual, I cannot get the meaning of the sentence 'For summary metrics, exclude GC windows that include less than this fraction of the genome'.
Hi,
The GATK support team is currently primarily focusing on resolving questions about GATK tool specific errors or abnormal results from the GATK tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and the tools.
We cannot guarantee a reply, however we ask other community members to help out if you know the answer.
For more information:
https://software.broadinstitute.org/gatk/blog?id=24419
https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1