Y R
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GATKgCNV References For Hg19 and Hg38
I cannot seem to find the recommended references by GATKgCNV for hg19 and hg38. I have used it before but I cannot find it currently. If this question is not allowed I can take it down. Does anyone...
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JexlEngine - ![0,14]: 'ReadPosRankSum < -20.0;' undefined variable ReadPosRankSum For GATK VariantFiltration
I am not sure if this question is allowed but I am having a bit of difficulty using the Variant Filtration command and I cannot seem to find a way around it. REQUIRED for all errors and issues: a) ...
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GATKgCNV Error: "Some contigs do not have ploidy priors"
The information is listed below: a) GATK version used: 4.4.0.0 using a singularity image whose path is stored under `singularity_image`.b) Exact commands used are below. I had a previous posting wh...
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GATK Index Feature FIle No suitable codecs found
AnsweredI am trying to get my Index Feature File from my bed file. I have used the command before and it worked but when I changed the bed file it stopped working. My GATK version used: 4.4.0.0. My Exact c...
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GATK "At least one interval must remain after intersection" For `FilterIntervals` Command
I am trying to follow the GATK g CNV protocol. I have an error from my `FilterIntervals` in GATK. It is in a for loop. I defined the following: - `bam_filename` is the name of the bam file - `coun...
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Is It Allowed To Submit An Entire Code For Review?
As I am working on GATKgCNV and trying to make a pipeline I was wondering if it is allowed to submit code here on this forum for review? I am still working on this pipeline.
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GATK sif file: "executable file not found in $PATH" When Path Is Correct For GATK g CNV
I am using GATK 4.4.0.0. (from docker) which I downloaded to an HPC using the following commands: ``` bash singularity pull docker://broadinstitute/gatk ``` I wanted to run GATK-g-CNV so I created ...
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Steps For GATK-gCNV pipleline on Exome Data
I am a bit confused as to the steps for GATK g-CNV and therefore I am making this post to understand it. I am dealing with multiple .bams as an input (so I believe I am supposed to use cohort mode)...