SeqMule: Automated human exome/genome variants detection

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.


  • Mendelian disease and cancer genome analysis

Suitable for both Mendelian disease study and tumor-normal paired somatic mutation analysis

  • Multiple aligners


  • Multiple variant callers

GATK, SAMtools, VarScan, SOAPsnp, Freebayes are available.

As stated on 1000 Genomes Project website, genotypes obtained through a consensus procedure are estimated to have 30% fewer errors than those generated by any single caller.

As we have demonstrated in a previous study (O'Rawe et al. Genome Med 2013, 5:28), consensus calls from multiple calling algorithms may increase calling accuracy and reduce Mendelian error rates.

  • Easy downloading and installation.

Most jobs can be done with one-line command.

  • Fast and easy customization

Just use predefined advanced_config or change it yourself!

  • Sun Grid Engine (SGE) integration

SeqMule is scalable and can utilize cluster computation resources managed by SGE.


  • seqmule download: download databases/BEDs that are required by sequence alignment or variant calling software tools

  • seqmule pipeline: perform the automated pipeline for detection of variants from whole-exome/genome data

  • seqmule stats: perform statistical analysis of variants data, such as drawing Venn diagram to examine overlap between VCF files, generating union/consensus ca lls, generating coverage/alignment statistics in specific genomic regions, calculating Mendelian error rates

  • seqmule run: continue run from last executed step after interruption or run from a specific step

  • seqmule update: perform automated update of the SeqMule software tools See doc/User Manual/Manuals for details

Revision History

For release history, please visit here. For details, please go here.


For questions/bugs/issues, please post on GitHub. In general, please do NOT send questions to our email. Your question may be very likely to help other users.

Please join SeqMule-dev for updates.


Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. SeqMule: automated human exome/genome variants detection. Scientific Reports, doi: 10.1038/srep14283, 2015

More information

Copyright 2014-2016 USC Wang Lab