2016-02-03 Yunfei Guo yunfeigu@usc.edu

  • Stability improvement
  • Documentation improvement


2016-01-07 Yunfei Guo yunfeigu@usc.edu

  • Default exome definition changed to RefSeq exon
  • Citation added (SeqMule published on Scientific Reports!)
  • Updated tutorials and FAQs
  • Bug fixes


2015-08-05 Yunfei Guo yunfeigu@usc.edu

  • Bug fixes


2015-07-09 Yunfei Guo yunfeigu@usc.edu

  • Added a public machine image (AMI) for running SeqMule on Amazon EC2, see RUNNING IN THE CLOUD in Tutorials.


2015-07-08 Yunfei Guo yunfeigu@usc.edu

  • SeqMule now supports somatic variant calling via SAMtools and VarScan2
  • Support for Sun Grid Engine
  • New job script format (no influence for end users)
  • New online help interface
  • Enhanced job scheduling and more concurrency


2015-02-13 Yunfei Guo yunfeigu@usc.edu

  • fixed a bug for file names containing whitespace.


2015-01-31 Yunfei Guo yunfeigu@usc.edu

  • Illumina TruSight Capture Kit BED files added
  • Replace Picard duplicate removal with SAMtools rmdup for faster speed
  • Improved runtime output
  • Bug fixes for /bin/sh, GATK3.3.0


2015-01-13 Kai Wang kaichop@gmail.com, Yunfei Guo yunfeigu@usc.edu

  • Add SNAP aligner for faster alignment
  • Better support for gzipped FASTQ input
  • Add Mendelian statistics calculation
  • Add variant normalization
  • Faster variant calling under quick mode
  • Add separate Venn diagrams for SNVs and non-SNVs
  • Better variant consensus generation
  • Improved stability
  • Bug fixes


2014-10-17 Yunfei Guo yunfeigu@usc.edu

  • Add '-tmpdir' option in 'seqmule stats' and 'seqmule pipeline'
  • Add 'seqmule update' to make allow automatic update.


2014-05-29 Yunfei Guo yunfeigu@usc.edu

  • Add GATK full version, Freebayes
  • Fix bugs related to multiple-sample variant calling
  • Improve performance under quick mode
  • Automatic detection and correction of chromosome naming across input
  • Other bug fixes