exomeseq-methods: use author year reference indicators

[johnbradley]

To improve ability for users to consume the methods reference switch to <author name> <year> superscript notation. From what I have read Markdown doesn't have an official way to specify superscript. The common practice is to use <sup>...</sup>.

[johnbradley]

Looks like the Name-Year uses parentheses instead of superscripts: https://writing.wisc.edu/Handbook/DocCSE_NameYear.html

[johnbradley]

Using name-year is difficult for citations that do not have a doi. In this example I used the package name but the results are less than satisfying:

# Methods:

DNA-Seq data was processed using the TrimGalore toolkit(trimgalore) (v0.4.4),
which employs Cutadapt(Martin 2011) (v1.14)
to trim low quality bases and Illumina sequencing adapters from the 3' end of the reads.
Reads were aligned to the b37 version of the human genome with the BWA3(Li and Durbin 2009) algorithm (v0.7.12)
Alignment processing and variant calling were performed using the GATK(DePristo et al. 2011) toolkit (v3.8)
following the Broad Institute's Best Practices Workflow(Van der Auwera et al. 2013) (July 2017).

# References:
- trimgalore. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
- Martin 2011. Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10. doi:10.14806/ej.17.1.200

- Li and Durbin 2009. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754–1760. doi:10.1093/bioinformatics/btp324

- DePristo et al. 2011. DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., … Daly, M. J. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43(5), 491–498. doi:10.1038/ng.806

- Van der Auwera et al. 2013. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline Van der Auwera GA, Carneiro M, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella K, Altshuler D, Gabriel S, DePristo M, 2013 CURRENT PROTOCOLS IN BIOINFORMATICS 43:11.10.1-11.10.33