about 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 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 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 ArticleThe error of the genomestrip's Svpreprocess
Hi,I'm just use the genomestrip to call the sv from pigs. I have 30 bams and then follow the introduction to prepare the reference file ,genomeMaskFile ,copyNumberMaskFile and ploidyMapFile files.But...
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...
View ArticleGenome STRIP SVPreprocess error
Hi I'm running genomestrip and I got this error I'm testing whole human genome to find out SVs with Genome STRiP. I used bwa, picard with Homo_sapiens_assembly38.fasta (GATK bundle) Here's my command...
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Error with no Description
Dear GenomeStrip team, My name is Elbay Aliyev. I am working as a Research Specialist at Sidra Medical and Research Center. We have huge project of 3000 Qatari Genome Project and we want to use...
View ArticleUsing GenomeStrip to genotype known vcf
Hi, I want to genotype known CNVs (from 1000G Phase3, GoNL, etc.) in our samples using GenomeStrip without performing any discovery step at first. 1) Do I have to run only the SVPreprocess steps...
View ArticleRegarding GenderMap file in genomestrip
Hello, Can someone tell me that what should i define gender for plant sample in gendermap file. Please explain me?? Thank you in Advance
View ArticleInvolving the svtoolkit/cookbook/.../set_sv_params.sh
I am running through the cookbook example given found at: http://software.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1 The set_sv_params.sh file needs to...
View ArticleRunning /scripts/genotype+sites.sh example/1000G_MERGED_DEL_2_99615.vcf rundir
An error occurred that I do not understand. `INFO 15:13:07,421 QScriptManager - Compiling 2 QScripts INFO 15:13:10,852 QScriptManager - Compilation complete ERROR -- ERROR stack trace...
View ArticleNew to GenomeSTRiP - Running Installtest Properly
So i am new to GenomeSTRiP. I have downloaded and extracted all the necessary pieces to run it and tried running the installtest. I ran the install test twice using two different commands, the first...
View ArticleinputFileIndexCache isn't defined error?
I am running the local example test run found in the cookbook. I have downloaded and unpacked all files properly. I have edited the necessary files to call the proper file folders. On each run, the...
View ArticleUsing Genome STRiP with data stored on a server
How would I go about running a genome set stored on a server when Genome Strip is on a local computer? Thank you.
View ArticleCNVDiscovery Troubleshooting
Hello, We are trying to use Genome Strip to process our data and seem to be encountering some errors when running CNVDiscovery. To assist with troubleshooting, a log file has been attached below....
View Articlemerge the output from SVgenotyper of genomestrip
Hello, I am running genometrip on genome sequencing data. i have 8 different varieties and i want to run genome strip for each species individually. after running the SVgenotype i got vcf file. Now,...
View ArticleSVDiscovery error: computeSampleLongMap
I have encountered a problem when I run SVDiscovery pipeline. # # # The script of SVDiscovery I had used is: !/bin/bash export SV_DIR=/work/SoftW/svtoolkit runDir=IEMS SV_TMPDIR=IEMS/tmpdir_SVDiscovery...
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