SVPreprocess error
Hi Bob and all, I try to use the GenomeSTRiP recently. I got some error while I am running SVPreprocess. I modify the installtest/discovery.sh as my svpreprocess script. Here are the script content :...
View ArticleIndel Realignment still needed for GenomeSTRiP?
Indel Realignment is no longer a recommended best practice step for the GATK pipeline to call genotypes with HaplotypeCaller. However, doesn't indel realignment still need to be run to prepare bams for...
View ArticleMetadata for Human b37
Hi, Do you have any plan to provide Human b37 reference metadata? Thanks!
View ArticleGenomeSTRiP Runtime Error: Cannot handle multiple junction records
I am getting the error message below when genotyping a list of deletions (generated by another sv program) with GenomeSTRiP.. Are there any workarounds/solutions for this? I am getting this error...
View ArticleStage 7 of CNVDiscoveryPipeline - all commands fail with...
I am attempting to run GenomeSTRiP's CNVDiscoveryPipeline. I have run SVPreprocess successfully and am now running CNVDiscoveryPipeline on a single chromosome. Each command at stage 7 fails with the...
View ArticleRunning GenomeSTRiP to genotype results in Out of Memory Error
How is the java heap space increased in a queue script to run MergeGenotyperOutput ? I tried running the command with -Xmx6g parameter but the script ran with a heap space of only 2048m. When running...
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 ArticleNot to generate final svdiscovery.dels.vcf
Hi All, I was running java -Xmx16g -cp ${classpath} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVDiscovery.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -cp ${classpath} \ -gatk...
View ArticleWhole Genome Sequencing and structural variation identification in human..
Hello, I have two queries regarding the structural variation identification using whole genome sequencing in human. If you can suggest, to identify structural variation (SV) like balanced chromosomal...
View ArticleGenerateHaploidCNVGenotypes error
Dear all After running CNVDiscoveryPipeline, I want to get the information of genotype for each sample. But when I running GenerateHaploidCNVGenotypes, an error occurred to me (like following). The...
View ArticleCan't decompress Genome STRiP tar.gz file normally
I downloaded both the latest versions of 2016 and 2017; both failed to be decompressed with `tar xzf svtoolkit_*.tar.gz' on Ubuntu 16.04 and 14.04: tar: This does not look like a tar archive tar:...
View ArticleTransloation detection on sex chromosome with one batch data?
We have a batch of data from 8 subjects generated with Ion Proton sequencer. We are interested in detecting translocation events in these subjects. We do not have reference data from other subjects....
View ArticleCNVDiscoveryPipeline 2 Jobs Fail
HI, Iam running GenomeStrip (lattest version) locally in a Docker-Container with wdl. I can run SVPrepross without any errors for my samples. For saving time I run GenomeStrip only on Chr11/14. When I...
View ArticleIs there Java version compatibility table, and can I download old versions of...
Thank you all for great software and active community. I'm trying to install and use but I faced a problem which someone already faced: Unsupported major.minor version 52.0 - do I need java 8? (howto)...
View ArticleMemory setting issue in CNV calling pipeline step 2: SVAltAlign
Hello, I failed in running CNV calling step 2: SVAltAlign, probably because of the memory setting issue. Even though the "-lsfMemLimit 128" is specified in the command, which is: "java -Xmx128g -cp...
View ArticleError when running CNVDiscoveryPipeline using the latest version(SVToolkit...
Dear @bhandsaker I have finished running the deletion discovery pipeline, but when running CNVDiscoveryPipeline using following command, it gave me an error. It is difficult for me to figure it out....
View Articlejava.lang.RuntimeException: Error processing input from file.bam: Invalid...
I'm getting the error above when I run Genome Strip discovery pipeline. I would appreciate help troubleshooting. Below are the lines in the output beginning with the first error through the end of the...
View ArticlesvGenotyper Error: Null Pointer
SVpreprocess seemed to run without error for my samples. However I'm getting an error with svGenotyper ##### ERROR...
View ArticleError Running CNVDiscovery Pipeline
I tried to run the pipeline and it succeeded for the first stage but then failed at the second. It looks like a null pointer exception. What other information would be useful to debug this? INFO...
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