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Release 0.1.3
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@tfenne tfenne released this 22 Feb 02:58
0.1.3
77e01b2

Release 0.1.3 introduces the following changes to existing tools:

  • CallMolecularConsensusReads now produces detailed information about consensus reads in new optional tags
  • MakeTwoSampleMixtureVcf now propogates the ID field from the source VCF into the mixutre VCF
  • ErrorRateByReadPosition now masks out known variants, provides per-substitution type error rates and produces summary plots
  • ReviewConsensusVariants now generates a detailed output file with a row per variant-supporting-read

In addition the following new tools were added:

  • ClipOverlappingReads: clips alignments from read pairs whose alignments overlap
  • FilterConsensusReads: filters consensus reads generated by CallMolecularConsensusReads
  • EstimatePoolingFractions: estimates the fractional contribution of individual samples with known genotypes to a pooled sample
  • EstimateRnaSeqInsertSize: estimates insert size distributions of RNA sequencing experiments in the presence of splicing
  • CallDuplexConsensusReads: generates consensus reads from duplex-sequencing protocols that embed a UMI at the start of each read in a pair
  • MakeMixtureVcf: generates a VCF for a mixture sample created from many individual samples
  • FilterSomaticVcf: applies filters to VCFs of somatic variants
  • RemoveSamTags: strips out optional tags/attributes from a SAM/BAM file to reduce size
  • ExtractBasecallingParamsForPicard: parses an Illumina Experiment Manager sample sheet and generates the files needed to run Picard's basecalling tools
  • ExtractIlluminaRunInfo: extracts information from Illumina's RunInfo.xml file into a simple tab-delimited table
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