Henry
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Activity overview
Latest activity by Henry-
Henry commented,
Hello, Gökalp Çelik ! Thank you for your rapidly reply, I read your adivce, but my issue does not matches your solution. I got a *vcf.stats file. I want to know if we generate Mutect vcf and vcf.s...
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Henry created a post,
FilterMuectCalls program request *vcf.stats file
REQUIRED for all errors and issues: a) GATK version used: GATK v4.5.0.0b) Exact command used: $java -XX:ParallelGCThreads=12 -Xmx80g -jar $gatk FilterMutectCalls -R ${reference} -V ${pairname}.vcf...
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Henry commented,
Hello, GATK team. I'd like to request assistance with resolving an error that I faced while using the GATK Annotator tool. I encountered an error "ava.lang.IllegalArgumentException: Null alleles ar...
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Henry commented,
I found the answer posting related my question! https://gatk.broadinstitute.org/hc/en-us/community/posts/360071895391-Speeding-up-GATK4-DepthOfCoverage To summarize this reply, 1. Depthofcoverage d...
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Henry commented,
Hello, GATK team ! I wonder that analysis speed of GATK - DepthOfCoverage.For DepthOfCoverage in GATK v3.4.0.0 the analysis threads could be adjusted with the -nt option.Is there no option in v4.5....
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Henry commented,
As you told me, I built a conda environment using the gatk4.4.0.0 gatkcondaenv.yml file. I kept checking for unknown errors. While trying to figure out the cause in many parts, I found out that th...
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Henry commented,
Thank you for helping me every time, Gökalp Çelik I followed your advice and proceeded with using gatk4 in python3 environment. I'm using the tool versions as below. java: jdk-17.0.5 gatk: 4.4.0....
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Henry commented,
Gökalp Çelik, Thank you for your replying, As following your advice, I exceuted scripts changed gatk 4.4.0.0 version. but, I saw new error message: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!...
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Henry created a post,
CNNScoreVariants, python timeout error occurred
REQUIRED for all errors and issues: a) GATK version used: gatk-4.0.5.1b) Exact command used: java -Xmx20g -Djava.io.tmpdir=./jtmp -jar gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar CNNScoreVariants ...
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Henry created a post,
SortSam - Question about I/O error
REQUIRED for all errors and issues:a) GATK version used:b) Exact command used:c) Entire program log: v.4.2.0.0 b) Exact command used: java -Xmx32g -jar /mnt/garnet/Tools/WGS_Analysis/Program/GATK/g...