Is there any on-line documentation about the software ?
What language(s) is the software written in ?
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 ?
Experiment - Run with other data
What input files does the software require ?
Same as the BAM files from SamtoolsBamIndex.
Input human reference genome file.
What are the input parameters used for this software?
What output files does the software produce ?
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 ?
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)