timh
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Latest activity by timh-
timh commented,
Thanks Genevieve. All right, sounds like I will automate something based on annotation stats. The --max-attempts function is usefull but the output file, which then contains multiple models, requir...
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timh created a post,
VQSR: how is insufficient variance inferred for annotations?
AnsweredHi there. Some of the annotations I use in VQSR do not always vary significantly and hence I get the following error: ```A USER ERROR has occurred: Positive training model failed to converge. One o...
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timh commented,
Hi. No I didn't change the R script.
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timh commented,
update: this appears to be the case for only a number of my datasets, works fine for others. So I am guessing the problem is not VQSR but my data, will have a closer look. Thanks
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timh commented,
Here you are: [exact command works without "-an AS_MQRankSum"] java -jar ~/Programs/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar VariantRecalibrator -R ref.fa -V test.4.1.4.1.vcf.gz -AS --resource:r...
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timh created a post,
postive AS_MQRankSum and VQSR
Hi. I have a technical question about AS_MQRankSum. As is mentioned in the info page in the tool section, positive scores for this measure are not really informative. I wonder how VQSR and ApplyVQS...
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timh created a post,
AS_MQRanksum craches R script VQSR
Hi. I am running GATK 4.1.4.1. and when I am running allele specific VQSR and include "-an AS_MQRankSum" I get the following error: 13:02:54.929 INFO VariantRecalibrator - Executing: Rscript /home/...