In nehiljain/genewiseR: A tool to perform pool gwas analysis in R,

Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The html_vignette output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The html_vignette format:

• Never uses retina figures
• Has a smaller default figure size
• Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style

Required software

1. to download test data from ncbi -- ncbi sra toolkit link
2. to trimming raw sequences -- flexbar link
3. to alignment -- bwa link
4. to utilities -- picard tools link
5. to utilities and mpileup -- samtools link
6. to prepare sync data and more -- popoolation2 link
7. to variant calling -- freebayes link and gatk link
8. to variant filtration -- snpsift link

Note the various macros within the vignette section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Test dataset

Pipeline

Data trimming

Alignment to reference

Aligned data preparation and mpileup

Popoolation2 - the core

Variant calling and filtration

Data reduction and CMH testing as final step to genewiseR

References

nehiljain/genewiseR documentation built on May 23, 2019, 1:31 p.m.