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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
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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.
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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