ERROR MESSAGE: Start cannot exceed end.
Hi support team. I meet an error when I am running the GenomesSTRiP. The error message is at below. ERROR ------------------------------------------------------------------------------------------...
View ArticleCN2 mask file for non human genome
Hi, I'm using genome strip with a non human organism. Before running it, I found I need to prepare CN2 mask file for the reference genome. I just wonder how to build my own, i.e., what rules should I...
View ArticleSVPreprocess
Hi Bob, When I run my SVpreprocessing I get an error saying: ERROR 10:44:12,666 FunctionEdge - Contents of .../svtoolkit/installtest/all/logs/SVPreprocess-6.out: INFO 09:57:47,537 HelpFormatter -...
View ArticleSVDiscovery
Hi Geraldine, I am using Genome STRiP in conjunction with other structural variant (SV) calling methods such as Breakdancer/Pindel to identify a list of SV calls based on Illumina sequence data from...
View ArticleRead pair records have different read groups ERROR
I am running GenomeSTRiP on 66 deep sequenced bam files. Of the 3147 runs during the discovery step, 11 failed with an error like this... SVDiscovery-113.out:java.lang.IllegalArgumentException: Read...
View ArticleOptimal batch sizes for GenomeSTRiP
How large a batch of bam files would be recommended for 40x coverage with the latest version of GenomeSTRiP? Presently we would like to run this on about 65 bam files initially. For discovery, is the...
View ArticleHow are a list of read groups excluded from discovery and genotyping
If the insert size distribution is not good for a list of read groups, what is the best way to drop them from the discovery and genotyping steps?
View ArticleError Message running Discovery-Input file is not sorted by start position
During the very last job of 3000+ jobs submitted with the Discovery qscript, the following error occurred running the VariantFiltration tool. ERROR MESSAGE: Input file is not sorted by start position....
View ArticleIs there a way to limit the genotyping to those sites with FILTER=PASS?
With the genotyping discovery qscript, all the discovery sites were genotyped during the run instead of the much smaller set that have filter=PASS. Instead of having all these sites genotyped, is there...
View ArticlePreprossing: Depth.dat file empty, Discovery: Error-No read count found
I'm running GenomeSTRiP with a modified version of the discovery.sh script from installtest. BAM files are all aligned to hg19, sorted with headers and have previously correctly run through the...
View ArticleCan't run GenomeSTRiP with "ploidyMapFile", "copyNumberMaskFile",...
Command line: java -cp ${classpath} \ org.broadinstitute.sting.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVPreprocess.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk...
View Article30x Genome GenomeSTRiP
Hi, Can you provide information on how long it would take to run a 30x human genome through GenomeSTRiP. Do you have details on run time, memory requirements, etc? Thanks.
View ArticleBAM file -O does not exist
Hi, I got an error when preprocessing: ERROR ------------------------------------------------------------------------------------------ ERROR stack trace...
View ArticleMeet an error when running GenomeStrip 1.04.1358 to call variants with exact...
Hi Bob, I met an error message when running GenomeStrip on the 50X data with multiple sample BAMs files ERROR ------------------------------------------------------------------------------------------...
View ArticleRight read of read pair fails right read test
Hello, I cannot find this particular error in any posted discussions. If the answer is already here, please direct me to it! These bams have survived without error a variety of processing and SNP...
View Articlefilter calls in regions of mostly alpha satellite repeat
Dear all, In discovery site filtering section of GenomeSTRiP tutorial, it is recommended to filter calls in alpha satellite repeat. I'm not familiar with repeat regions in the genome. Why is it better...
View Articlemetadata included in the cookbook cannot be found
Hi there, I was trying to follow the example described in the cookbook (http://www.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1). However, the metadata...
View ArticlegenomeSTRiP breakpoint refinement
Hi, Bob I'm using tigra and age to refine the breakpoint of deletions discovered by GenomeSTRiP. And I find that with a large deletion, it always tends to be a micro-insertion (e.g. 1 bp or 2 bp) or a...
View Articleproblem with java connection
Hi there, I was trying the genotyping example provided in the cookbook. And I got java connection error. The error message is as follows: ERROR 15:08:11,690 SAMUrlLocation - Error reading from the URL:...
View ArticleHow to run GenomeStrip for a small set of high coverage data
Hi, I have high coverage(~40X) bam files of 6 samples(2 trio), and all the bam files are mapped to hg19. And I notice it needs at least 20-30 samples to run GenomeStrip. If I split these 6 bams...
View Article