Frequently Asked Questions
1. What does error message X mean? See the FAQ section on frequently encountered errors. 2. Can I use Genome STRiP to do discovery or genotyping in a single high-coverage individual? Genome STRiP is...
View ArticleFrequently Asked Questions - Specific Errors
1. SVGenotyper ERROR MESSAGE: Please invoke this walker with -BTI This can be caused by an incorrect invocation of the command or a malformed input file. The SVGenotyper walker requires the GATK -BTI...
View ArticleGenome Mask Files
1. Introduction Genome STRiP makes use of mask files that identify portions of the reference sequence that are not reliably alignable. Genome mask files are fasta files with the same number of...
View ArticleGenerateAltAlleleFasta
1. Introduction The GenerateAltAlleleFasta utility processes a VCF file to extract the sequences of the alternate alleles. For each structural variation record in the VCF, this utility will generate...
View ArticleComputeReadSpanCoverage
1. Introduction The ComputeReadSpanCoverage walker traverses a set of BAM files to generate genome-wide statistics. The read span coverage is the count of bases in between two paired-end reads, not...
View ArticleComputeInsertStatistics
1. Introduction The ComputeInsertStatistics utility prints statistics about the data in a binary histogram file. The printed metrics include the median insert size and robust standard deviation (RSD)....
View ArticleComputeInsertSizeDistributions
1. Introduction The ComputeInsertSizeDistributions walker traverses a set of BAM files to generate histograms of insert sizes. The insert size histograms are stored in a binary file format. Many...
View ArticleComputeGenomeMaskStatistics
1. Introduction The ComputeGenomeMaskStatistics utility prints the number of alignable and unalignable bases. See ComputeGenomeMask. 2. Inputs / Arguments -I <mask-file> : The genome mask file....
View ArticleComputeGenomeMask
1. Introduction The ComputeGenomeMask utility determines the alignability of each base in the reference genome. Mask files are generated based on a fixed read length L. A base is considered alignable...
View ArticleMergeDiscoveryOutput
1. Introduction The MergeDiscoveryOutput utility merges the results of a parallel discovery run into genome-wide output files. In addition to merging the main VCF files, this utility will also merge...
View ArticleMergeGenotyperOutput
1. Introduction The MergeGenotyperOutput utility merges the results of a parallel genotyping run into genome-wide output files. In addition to merging the main VCF files, this utility will also merge...
View ArticleMergeInsertSizeDistributions
1. Introduction The MergeInsertSizeDistributions utility combines multiple insert size histogram files into one. The insert size histograms are stored in a binary file format. 2. Inputs / Arguments -I...
View ArticleMergeReadSpanCoverage
1. Introduction The MergeReadSpanCoverage utility merges files containing read span counts into one file. This utility is used for parallelizing computation of read span coverage. See also...
View ArticleMergeReadDepthCoverage
1. Introduction The MergeReadDepthCoverage utility merges files containing read depth counts into one file. This utility is used for parallelizing computation of read depth coverage. See also...
View ArticlePlotGenotypingResults
1. Introduction The PlotGenotypingResults utility produces plots that help to visualize the genotyping data for individual sites. The plots show a histogram of read depth, decorated with information...
View ArticlePlotInsertSizeDistributions
1. Introduction The PlotInsertSizeDistributions generates plots of the insert size distributions of each sequencing library. For sequencing libraries with paired reads, one can measure the empirical...
View ArticleSuperArray
1. Introduction The SuperArray annotator is invoked through the SVVariantAnnotator walker, which defines arguments common to all annotators. The SuperArray annotator uses array intensity data to do a...
View ArticleSVAltAlign Queue script
1. Introduction SVAltAlign.q is a sample Queue script that is part of Genome STRiP. This script realigned previously unmapped reads against putative alternate alleles generated from a VCF file...
View ArticleSVAltAligner walker
1. Introduction The SVAltAligner walker traverses a set of BAM files to compute alignments to the alternate alleles of structural variations. This walker is one component of the SVAltAlign pipeline. 2....
View ArticleSVDiscovery Queue script
1. Introduction SVDiscovery.q is a sample Queue script that is part of Genome STRiP. This script runs deletion discovery over an input data set based on a set of bam files. The input bam files must...
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