zhao shilin
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Activity overview
Latest activity by zhao shilin-
zhao shilin created a post,
mutect2 non reference allele in normal
Hello, I am working on somatic mutation identification in mouse. The mouse strain I am working on is different than mm10 so it has a lot of germline SNPs. I am trying to call somatic mutation in tu...
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zhao shilin commented,
Thanks! For Q5, I found it is related to permission issue in singularity (I am using singularity image in HPC, which was converted from docker image). There is a root folder in singularity image b...
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zhao shilin commented,
Thanks for your very clear reply. For Q4, may I know how you will analyze a group of samples? For example, you have a few tumor samples from different patients, you will use MuTect2 to call somati...
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zhao shilin created a post,
mutect2 multi-sample
AnsweredHello, I am trying to use the mutect2 multi-sample feature. As it is relatively new, I didn't find many documents about it. Would you please help to clarify a few questions? 1. If I understand it c...
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zhao shilin commented,
Hello Tiffany, as mentioned above, broadinstitute/gatk:4.1.4.0., 4.1.2.0 and 4.1.0.0 are not working. gatk_4.0.1.1 works. All dockers were downloaded from docker hub and made into singularity image...
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zhao shilin commented,
Tested gatk_4.0.1.1 docker and it worked (in fact downloaded docker and made it a singularity image) as this version was mentioned in https://gatk.broadinstitute.org/hc/en-us/articles/360035531092?...
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zhao shilin commented,
Yes, other task wdl (such as pre-processing) works. I am using the json file in the same github with changes about file locations as all the files (bam and reference) were located at HPC's storage ...
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zhao shilin commented,
it is not a same issue/question but also related to gatk docker. https://github.com/gatk-workflows/gatk4-somatic-cnvs/issues/16
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zhao shilin commented,
Hello Tiffany, Thanks for your reply. I am following the workflow at https://github.com/gatk-workflows/gatk4-somatic-cnvs. Based on the json file, it is broadinstitute/gatk:4.1.4.0. I also tested s...
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zhao shilin created a post,
docker CreateReadCountPanelOfNormals cblas_dspr error
If running CreateReadCountPanelOfNormals from workflow in GATK docker, it has the same issue as mentioned in other posts https://gatkforums.broadinstitute.org/gatk/discussion/12537/get-error-when-u...