What's new in USeq 8.9.6
Jan 6, 2016
- Sam2USeq:
- Modified the per region spreadsheet to show the FracBPs>= xxx to be defined by the users minimum coverage setting.
- Now gzipping pass and fail bed file outputs
- MatchMates:
- New app for joining second of pair alignments to their first of pair attributes fields. Use with FastqBarcodeTagger and Consensus.
- Consensus:
- New app that clusters alignments by position and molecular barcode then calls consensus on the clustered alignments outputing fastq for realignment.
New in USeq 8.9.5 (Jan 6, 2016)
- Sam2USeq
- Added a failed bed region output for those target bases with less than the indicated depth. Good for identifying holes in particular locations, and deletions.
- Sam2USeq, CalculatePerCycleErrorRate, SamAlignmentExtractor, MergePairedAlignments
- Added option to export key QC metrics in json format
- Moved base summary stats to MergePairedAlignments to get a more accurate uniOb count for total, Q20, and Q30
- MergeRegions
- Fixed issue of running this on java 1.7+ with contract sort violation
- MpileupParser
- New App for parsing a SAMTools mpileup output file for non reference bases generating PointData for the reference, non reference, and fraction non reference for bases that pass the minimum read coverage filter.
- Histogram
- Changed counters to use long instead of int to avoid overflow, this affects ~10 apps
- MultiSampleVCFFilter
- Fixed an issue with filtering records that contain no genotype quality GQ field. These were being failed and removed.
- FastqBarcodeTagger
- New app for adding barcode reads from a third fastq file to paired fastq file headers, supports interlaced output for direct piping into downstream apps (recommended).
New in USeq 8.9.4 (Jan 6, 2016)
- SamAlignmentExtractor
- Rewrote the app to enable processing deep coverage datasets without exceeding memory requirements. Added lots of QC metrics.
- BamBlaster
- New app for injecting snv and indel variants from a vcf file into a bam file
- BamMixer
- New app for mixing BamBlaster alignments into different frequency tumor samples
- VCFMutationMaker
- New app to generate vcf files with random snvs and indels over target regions for BamBlaster
New in USeq 8.9.3 (Jun 8, 2015)
- Bed2UCSCRefFlat:
- New app for converting a bed file to a multi exonic UCSC RefFlat file.
- Sam2USeq:
- Fixed an issue where chromData from the MergePairedAlignments app fail to cal read coverage with b37 no "chr" data. Now must match the bed file with the alignments.
New in USeq 8.9.2 (Apr 16, 2015)
- New app for detecting CNV variants in large sets of exon or gene capture panels. Wraps an algorithm by Alun Thomas.
New in USeq 8.8.9 (Feb 25, 2015)
- FilterIntersectingRegions:
- Added a max gap option and support for splitting ucsc ref flat files.
- MergeOverlappingGenes:
- Merges transcript models that share a minimum fraction exonic bps. Good for collapsing Cufflinks transcripts.
- VCFComparator:
- More modifications to support bed format variant info for somatic key test analysis
- MultiSampleVCFFilter:
- Fixed issue with processing gzipped vcf files when a tabix exe isn't provided
- SomaticSniperVCFParser:
- New app for inserting quality score into QUAL field and option for score filtering
- VCFNoCallFilter:
- New app for removing vcf records where too few background samples pass QC or are no calls. Better than filtering by capture target region.
- MuTechVCFParser, SomaticSniperVCFParser, StrelkaVCFParser:
- New apps for manipulating these flavors of vcf files
New in USeq 8.8.8 (Dec 20, 2014)
- VCFComparator:
- Major bug fix! The filter for selecting vcf variants for those in common regions was inadvertently disabled. Ugg! To findout if your prior analysis as affected, look at the # of pre and post filtered variants these should differ, if not discard!
New in USeq 8.8.7 (Dec 16, 2014)
- ReadCoverageParser:
- Renamed to CollectBamStats
- Added a bunch of functionality to collect both read coverage data and alignment stats from the MergePairedAlignments and Sam2USeq apps
- MergePairedAlignments:
- Threaded app, generates ChromData for direct import into Sam2USeq; 3x faster overall.
- DefinedRegionDifferentialSeq:
- Updated DESeq2 scripts to support latest rlog method names
- Added option to disable independent filtering
- Several apps dependent on the POI Excel library:
- Updated the POI classes to work, was causing several apps to error out on launch.
- VarScanVCFParser:
- Fixed an issue where the ssc score wasn't getting copied into the QUAL field
New in USeq 8.8.6 (Dec 5, 2014)
- Added another catch for missing stranded datasets from targeted capture experiments that were throwing null pointer errors.
- BisStatRegionMaker:
- Added option to set R path.
- Sam2USeq:
- Added option to output base level read coverage PointData in bar format for
- AggregatePlotter:
- CalculatePerCycleErrorRate
- Added option to process 1st and 2nd reads separately
- ReadCoverageParser:
- Parses output of Sam2USeq to plot many read coverage plots and flag samples that fail set thresholds for coverage
- MergePairedAlignments:
- New app focused on H1K QC. Works with either queryname or coordinate sorted bams.
- VCFComparator
- Added option to use a bed file of key variants instead of a vcf file to allow wiggle in BamSurgeon generated variants
New in USeq 8.8.5 (Oct 31, 2014)
- CHANGES:
- Added option to filter by region
- Cleaned up chunking issues when no chunking is indicated
- VarScanVCFParser:
- New app to extract SOMATIC calls and replace QUAL score with the ssc score.
- SamAlignmentExtractor:
- Added option to output alignments that don't intersect the regions.
- BamSurgeonMutator:
- Generates random mutations in a list of regions for the BamSurgeon application
- BisStat:
- Fixed an issue where some runs were throwing a comparator contract sort error due to lack of data in a particular base context and thus null fraction values
New in USeq 8.8.4 (Oct 16, 2014)
- MergeSams:
- Created a new app to merge sam and bam files. Creates a stripped header from the files if one isn't provided. This won't play nicely with downstream GATK or Picard apps. Have yet to find at good app for doing this, SamTools and Picard's are riddled with error/ validation headaches.
- DefinedRegionDifferentialSeq:
- Added catch for alignments that are run off the end of the last reported base in a chromosome
- SamSplitter:
- New app for splitting a sam file in half. Randomly assigns paired read groups to either half.
- VCFComparator:
- Removed requirement that read depths are provided for the alleles. Added a skip for finding common regions when the same bed file is provided.
New in USeq 8.8.3 (Sep 19, 2014)
- VCFComparator
- Added option to ignore the alt comparison when scoring whether the test and key match. Thus just scores the position.
- Fixed an issue where SNP's with two alternates were called as a non SNP.
- Telescriptor
- Added new app to score two transcriptomes for possible telescripting and 3' UTR changes
- DefinedRegionDifferentialSeq
- Added patch to fix DESeq2 rLog method call.
New in USeq 8.8.2 (Aug 7, 2014)
- ReferenceMutator
- New app that takes a directory of fasta chromosome sequence files and converts the reference allele to the alternate provided by a snp mapping table.
- SamComparator
- New app that compares two sam/bam files and splits those into matching and non matching based on coordinates. Good for allele specific expression analysis.
- DefinedRegionDifferentialSeq
- Added option to collect counts from the 5' and 3' ends of genes
- DifferentialReadCoverageComparator
- Takes the count table generated by DRDS with the -z option and looks for changes in 5'/3' read coverage between different conditions to identify short truncated transcripts
- RandomMutationGenerator
- Creates snvs and indels for the BAMSurgeon application
New in USeq 8.8.1 (May 23, 2014)
- VCFSpliceAnnotator
- Relaxed the thresholds for calling a novel or damaging an existing splice junction
- ChIPSeq, RNASeq, MultipleReplicaScanSeqs.
- Updated each to utilize the new DESeq2 algorithm.
New in USeq 8.8.0 (May 12, 2014)
- Updated DESeq to DESeq2, major changes, different dispersion fit, different log2Rto calculation, automatic independence filtering. All results in more diff expressed genes compared to the older depreciated methods. Old diff genes are pretty much a subset of new diff genes.
New in USeq 4.1 (Jul 10, 2009)
- Officially added the GUI.
- Added a new application for merging two microarray designs (FilterIntersectingRegions). Modified Alleler output for generating bed files from INDELS.
New in USeq 4.0 (Jun 26, 2009)
- Modified the FilterDuplicateAlignments app to enable unique sequence selection.
- Added a new app for rapid intersection of two microarray designs.
New in USeq 3.9 (Jun 19, 2009)
- Added several applications to assist in the design of capture/ release -> sequencing microarrays.
- Added instructions for such to the user guide.
New in USeq 3.8 (Jun 17, 2009)
- Fixed an error in the ReadCoverage application, negative stranded reads were being shifted 1/2 the read length in the wrong direction.
New in USeq 3.7 (Jun 12, 2009)
- Added several apps needed for generating cap-seq arrays, made many additions to the OligoTiler application to speed array design through Agilent eArray.
New in USeq 3.4 (May 12, 2009)
- Fixed reporting bug in DefinedRegionScanSeqs when using bed files.
New in USeq 3.3 (May 11, 2009)
- Added a catch for cases when the R qvalue estimation returns infinity.
New in USeq 3.2 (May 8, 2009)
- Bug fix for qValueFDR estimation in ScanSeqs, inadvertently disabled this feature in prior release. Updated documentation.
New in USeq 3.1 (May 4, 2009)
- Upgrade of the q-value FDR estimation in ScanSeqs and DefinedRegionScanSeqs. Much better accuracy through the use of fuzzy p-values for trials with < 20 observations.