Can we use GenomeSTRiP on Whole Exome Sequencing Data
Can we use GenomeSTRiP on whole exome data as well?
View ArticleGenomeSTRiP for duplication
Hi bob, I used the latest version to run CNV calling on a population samples (ten individuals) from 1000 genome. After running the process, discovery and genotyping according to the tutorials,...
View ArticleIRS TEST
Hi everyone, It is very nice to use the chip intensity data to estimate the FDR of the discovered CNVs. But the algorithm implemented in the GenomeStrip is difficult for me to understand when a CNVR...
View ArticleUnable to determine status of job ID error
Hi, I occasionally get the following type of error when using genome strip CNVDisvovery pipeline on a cluster running SGE, it will run successfully for long periods of time and then arrive at this type...
View ArticleCNVDiscovery Error: Could Not Find Function arrow
Hi all, at the very end of the CNVDiscovery pipeline I get the following RScript error, but I'm unsure of why it might occur. It seems to fail to find the arrow function, part of the grid package which...
View ArticleGStrip discovery: java heap space?
Hi, I'm having a recurrent problem at the Discovering deletions stage. The error message states out of memory but I'm wondering if it isn't caused by an error in my code. I'm not sure how the " export...
View ArticleUnable to submit job
Hi, Bob I'm trying to use GenomeSTRiP to call CNV. While running CNV discovery with the command below: java -Xmx4g -cp ${classpath} \ org.broadinstitute.gatk.queue.QCommandLine \ -S...
View ArticleGS working on melanogaster but...
Hi, I've managed to get my deletion caller to generate a genotypes.vcf with complete calls, running on 20 flies, covering 2 million bases, search for events between 100bp and 10,000 bp. This detects...
View ArticleNo discovery.vcf when vars change
Hi, As suggested in the title, I successfully ran the deletion calling pipeline to completion on 20 individuals, 2 million contiguous, autosomal bases, 100-10,000bp in length. However, when I run the...
View ArticleCan GenomeStrip work on species without sex chromosomes?
Hi, Can GenomeStrip work on species without sex chromosomes? e.g yeast. Cheers, Will
View ArticleGenomeSTRiP or Queue used grid program
Hi. I'm Sunhye My lab will convert SGE to HTCondor. So, I wonder whether GenomeSTRiP or Queue (GATK) support HTCondor or not? To use GenomeSTRiP, do I need only SGE or LSF?
View ArticleUsing hs37d5 genome to call SVs on data aligned with hg19
Hi, I need help please. SO my question here is does the message below has to do with the fact that I happened to call SVs on hg19 aligned data with the HS37D5 genome? If so how can I fix it without...
View Articleproblem generating x.unfiltered.vcf
Hi, I'm running GS/2.0 deletion detection and genotyping pipeline on 222 samples, 180Mb whole-genome Illumina, 30X coverage. Even after I've fixed all my other problems, I still get this...
View Articleerror when merge discovery output
Dear GenomeSTRiP developer, I've run the svdiscovery script and it hangs on after all individual SV detection finished. The error message I've got is the following: INFO 23:14:42,482 HelpFormatter -...
View ArticleGenomeSTRIP slow
Hi all, Recently, I am trying to identify CNV(100k ~ 10MB) from PE data with GenomeSTRIP. I followed the instruction...
View ArticleCNV pipeline on SGE
Hi, I've got my deletion pipeline working on D.melanogaster, by running discovery on the major chromosomes separately, (and ignoring the unmapped scaffolds that I think were causing the problem). I'm...
View Articlegenotyping CNVs
Hi @bhandsaker , I run 220 samples, 1 chromosome through the CNV discovery pipeline on recommended settings which generates this vcf gs_cnv.genotypes.vcf.gz, comprising of the metrics for each genotype...
View ArticleDeletion QC plots
Hi @bhandsaker I'm inspecting my results from the Genomestrip/2.0 deletion pipeline: 244 of them reported on one 23Mb chromosome in 221 flies, at 20-40X coverage. Attached is a density distribution...
View ArticleSVPreprocess sequencial failure
Hello, I am running pre-processing script given below : # java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVPreprocess.q \ -S...
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