Release notes Biopet version 0.3.0

Since our first release in December 2014 many new functions have been added to the pipelines including: - Multisample compatibility - Summary framework - Md5sum of all input/output files ( need to be provided in the summary ) - Sequence stats - Program stats/versions - mapping stats - Tool stats ( if pipeline uses a biopet tool, it will output the version of the tool and all other statistics that might be captured ) - A entire new pipeline named Gentrap based on our previous Makefile version, with extra features like: - remove all ribosomal reads - multi sample runs - GATK VariantCalling has a lot of new features and is now called Shiva - Annotation pipeline ( development version )

Also a impressive list of tools have been added to the updated framework:

  • AnnotateVcfWithBed ( This enables the user to Annotate a VCF file based on a bed file containing the locations of interest )
  • CheckAllelesVcfInBam
  • ExtractAlignedFastq
  • FastqSplitter
  • FastqSync
  • MergeTables
  • SamplesTsvToJson
  • Seqstat ( this is a lift over tool based on our previous python implementation of seqstat )
  • VepNormalizer ( This normalizer enables a user to parse VEP output VCFs to the exact specs of VCF 4.1 )
  • VcfStats

Some tools have a new version for better compatibility with our latest pipelines. The tools that have a changed version are: - FastQC v0.11.2 - seqTK Version: 1.0-r63-dirty - sickle version 1.33 - Cutadapt 1.5 - GSNAP version 2014-12-22 - TopHat v2.0.13 - cufflinks v2.2.1 - HTseq-count version 0.6.1p1 - pdfTeX, Version 3.1415926-2.5-1.40.14 (pdflatex) - R scripting front-end version 3.1.1 (2014-07-10) (Rscript) - tabix Version: 0.2.5 (r1005) - grep (GNU grep) 2.16 - gzip 1.6 - Samtools Version: 1.1