v1.2.5
2016-02-03 Yunfei Guo yunfeigu@usc.edu
- Stability improvement
- Documentation improvement
v1.2.4
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
v1.2.2
2015-08-05 Yunfei Guo yunfeigu@usc.edu
- Bug fixes
v1.2.1
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.
v1.2.0
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
v1.1.4
2015-02-13 Yunfei Guo yunfeigu@usc.edu
- fixed a bug for file names containing whitespace.
v1.1.3
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
v1.1.2
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
v1.1.1
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.
v1.1.0
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