This workflow was implemented using the old pre-1.0 version of gwf that has now been retired and is no longer available for download. I will keep this repository as it is to document the analysis that was used in the article. But I am working on simplifying the mutation rate calling workflow and updating it the current version of gwf, so if you are interested in running this workflow on a new data set you should send me an email asking about the progress of that updated version.
- Pedigree of samples
- a bam-file for each sample
- reference genome in fasta format and 2bit format
- samtools
- GATK
- Python, including the following packages:
- bx-python
- PyVCF
- R, including the following packages:
- dplyr