MpileupCaller [Heng Li]


Locate - Unique description

  • What is the software called ?
    • MpileupCaller
  • What is a short description for this software ?
    • Records alignments by sample and calls variants from RNA/DNA sequencing data based on the input parameters
  • What are general categories (keywords, labels) for this software ?
    • samtools
    • omics
  • Is there a project website for the software ?
  • [OPTIONAL] What is the DOI or any other unique identifier for this software (or software version) ?


    Trust - Quality and ratings

    • Who created this software? (Project, Organization, Person, Initiative, etc.)
      • Heng Li
    • Are there any additional contributors of note for this software ?
      • John Marshall
      • Petr Danecek
    • What useful features of this software are worth highlighting ?
      • [OPTIONAL] Who is the publisher of this software if not the author ?
        • [OPTIONAL] How can a user get support for the software ? (eg. Report bugs, request features and extensions, etc)
          • [OPTIONAL] Has the software been adopted in a project, organization or by a person?
            • [OPTIONAL] Is there any information about uses of this software (papers, research labs, etc) ?
              • [OPTIONAL] Are there any statistics of its use ?
                • [OPTIONAL] Are there any publications where the software is used ?
                  • [OPTIONAL] Is there any benchmark information about the software ?
                    • [OPTIONAL] What are the funding sources for this software?
                      • [OPTIONAL] What are the ratings for this software?

                        Relate - Domain knowledge

                        • What are domain specific keywords for this software ? (eg: hydrology, climate)
                          • [OPTIONAL] Is there any other similar software that you know of ?
                            • [OPTIONAL] What are the recommended uses and assumptions for the software ?
                              • [OPTIONAL] Are there any constraints on use, situations it is not designed for, simplifications ?


                                Access - Download

                                Install - Execution requirements

                                • Is there any on-line documentation about the software ?
                                  • What language(s) is the software written in ?
                                    • C
                                  • What Operating Systems can the software run on ?
                                    • How can one install the software ?
                                      • What other software does the software require to be installed ?
                                        • [OPTIONAL] Are there estimates of how long it takes to run this software on average ?
                                          • [OPTIONAL] Are there any memory requirements for this software ?
                                            • [OPTIONAL] Are there any other important details about the implementation of this code (parallelization, special hardware, etc) ?

                                              Run - Testing execution

                                              • Is there any test data available for the software ?
                                                • [OPTIONAL] Are there any specific instructions for testing the software ?

                                                  DO RESEARCH

                                                  Experiment - Run with other data

                                                  • What input files does the software require ?
                                                      • File Id: 
                                                      • File Type: 
                                                        Same as the BAM files from SamtoolsBamIndex.
                                                      • File Id: 
                                                      • File Type: 
                                                        Input human reference genome file.
                                                  • What are the input parameters used for this software?
                                                    • minAlignmentMappingQuality
                                                    • minGappedReads
                                                    • minBaseQuality
                                                  • What output files does the software produce ?
                                                      • File Id: 
                                                      • File Type: 
                                                        A VCF (“Variant Calling Format” File) withe genotype likelihood and chromosomal positions which are “called” as mutations by the samtools pileup function. There are two types of VCF files - one with mutation info and one with high-level. This is intermediary file with less info
                                                  • [OPTIONAL] Are there any relevant data catalogs that can be used with this software ?

                                                    Compose - Run with other software

                                                    • What other software can interoperate with this one?
                                                      • [OPTIONAL] Is this software typically used with other software in a workflow ? (eg: for visualization, preprocessing, postprocessing, etc)

                                                        Cite - Scientific publications

                                                        • Is there a preferred publication or citation for this software ?

                                                          GET SUPPORT

                                                          Discuss - Support and community

                                                          • What is the e-mail contact for this software?
                                                            • [OPTIONAL] What is the support offered for this software?


                                                              Contribute - Evolution

                                                              • [OPTIONAL] How is the software being developed or maintained ?
                                                                • [OPTIONAL] Are there any on-line resources for accessing the developer community for this software ? (eg. discussion board, wiki, etc)

                                                                  Track - Versions

                                                                  • What versions does the software have ?