IDENTIFY

What is the software called ?
- SamtoolsBamIndex
What is a short description for this software ?
- Index bam file. Required for smoothly calling variants. Software: “samtools”; Function used in the run script: “index”
What are general categories (keywords, labels) for this software ?
- samtools
Is there a project website for the software ?
- http://www.htslib.org/doc/samtools.html
[OPTIONAL] What is the DOI or any other unique identifier for this software (or software version) ?

UNDERSTAND

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?

What are domain specific keywords for this software ? (eg: hydrology, climate)
- bioinformatics
[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 ?

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 ?
- Unix
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) ?

What input files does the software require ?
- - File Id:
    inputBamFile
  - File Type:
    BAM (binary alignment format) files are. The input file can be reads successfully aligned to the genome/ reads that were not mapped. Standard for Next generation sequencing data.
What are the input parameters used for this software?
What output files does the software produce ?
- - File Id:
    outputBamIndexFile
  - File Type:
    The file with “indices” of the BAM file. This contains information of what sequences mapped/ did not map to the genome. The output filename from WiINGS is a dummy/black file because the samtools index file is “required” to have the same name as the inputBamFile but with “bai” extension.
[OPTIONAL] Are there any relevant data catalogs that can be used with this 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)

[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)