SV annotation using SVAnnotator in GenomeSTRiP2.0
Hi. I got SV.vcf using GenomeSTRiP2.0 then annotated this file using SVAnnotator. In AlleleFrequency.report.dat, POPULATION column contains "NA" not "Nation" In AlleleFrequency.report.dat, ID PLOIDY...
View ArticleIssue with -jobNative option
Hi, I'm trying to run genomestrip on a UGE cluster. I would like to export my current environment using -jobNative "-V", but I get this error: ##### ERROR...
View ArticleWhat is the best way to limit the number of running jobs in genomestrip?
Previously, I had used -qsub -parallelJobs 5 to limit the number of simultaneously running jobs, but I have been told using the -qsub flag is not preferable: @bhandsaker said: Also, you probably do not...
View ArticleCNVDiscoveryPipeline failed in stage 1
Hi, I met an error on running CNVDiscoveryPipeline in the first stage, seems because of reaching LSF memory usage limit: Here is the log file: " ERROR 15:53:48,754 FunctionEdge - Error: 'java'...
View ArticleUnable to load library 'drmaa': libdrmaa.so error
Hi, After specifying -jobRunner Drmaa and -gatkJobRunner Drmaa and changing LD_LIBRARY_PATH for my CNV Discovery script, when I try to run the script, I get the error "ERROR 22:38:50,102 QGraph -...
View Articlegender mask bed file vs gender map file
Hi, In the documentation for SVPreprocess (http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_SVPreprocess.html), there is an advanced parameter -genderMaskBedFile, but in...
View ArticleSVPreprocess.qError: Cannot determine library identifier for read...
Hi , I have a bam file without library name , although each bam file is one library. The SVPreprocess.q throws a warning and an error in the ComputeInsertSizeHistogramsWalker and ComputeGCProfileWalker...
View ArticleSVPreprocess error following ReduceInsertSizeHistograms
Hi, When I try to run SVPreprocess, I am getting the following error multiple times, each for different sample files: ERROR 13:56:09,433 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC'...
View Articleabout CopyNumberClassAnnotator, AlleleFrequencyAnnotator
Hi. I have 3 questions. I wonder what CNCATEGORY means in CopyNumberClassAnnotator's output. For SVGenotyper's out, I run to annotate using CopyNumberClassAnnotator. First, What do "NA" in CNCATEGORY...
View ArticleWhat would be the correct approach to simulate reads from two parents?
I have simulated pair end reads from two parental lines. These reads were combined to simulate an F1 cross. Later I aligned the reads with one of the parents and generate the BAM files that were then...
View ArticleWhich memory and temporary storage need to run GenomeSTRIP...
Hi, I would like to run CNVDiscoveryPipeline of GenomeSTRIP on 87To of CRAM files (about 3000 human being). I understand that the step 5 of the pipeline need to use together data from several BAM files...
View ArticleGeneOverlapAnnotator
Hi, I wonder where I can find the SortGTFFile utility program? The link on the webpage http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_annotation_GeneOverlapAnnotator.html is...
View Articlecan GenomeSTRIP 2 detect the CNV for sequences that are in multiple copies in...
Hi, I tried to run CNVDiscoveryPipeline to discover CNV in my samples. To check that the pipeline work well, I looked at a region that contains a gene (size = about 2,500nt) that has different copy...
View ArticleGenomestrip for Drosophila
Other than the reference sequence, I'm assuming that the most significant edit that I have to make to the standard protocol, is changing the genome sizes (from human to fly) in the parameters file. The...
View Articlethree g-strip questions
Hi, My workflow is for unrelated individuals, in model organism, with many small unmapped contigs high in heterochromatin. No genotype calls are being generated in final genotyped vcf. Lots of LQ...
View ArticleSVPreprocess: memory issue and -jobNative options
Hi, I'm trying to process 150 WGS 30X BAMs in one batch. 5 samples failed due to "TERM_MEMLIMIT: job killed after reaching LSF memory usage limit." I have some questions. 1) In one thread you said that...
View Articlegender and/or R problem ?
Hi, My deletion calling pipeline runs to completion but there are error messages (see below). The first error message points to SVDiscovery-1.out which contains the error message on .R: Error in...
View ArticleThe length of the SV and CNV using GenomeSTRiP and the state of Input data
Hi. I have two question. First, using GenomeSTRiP2.0, I wonder what the range of the length of a reliable SV and CNV is. Does GenomeSTRiP have the limit on the length of SV and CNV? for example, by...
View ArticleClik here to view.
Annotated results of SVDiscovery: singletons?
I annotated a SVDiscovery/SVGenotyper output VCF file using VariantsPerSampleAnnotator. Out of a cohort n=50 I got 2 samples (sample A and sample which have singletons on chr7 (1 singleton per each...
View ArticleArgument with name '--tilingwindowsize' (-tilingWindowSize) is missing
Hi, I met error about GenomeStrip2.0 CNVDiscoveryPipeline. Some parts of the error log are as following, However, I am not able to fix it by myself, could you help? Thanks so much! SVToolkit version...
View Article