Code and scripts used in my (RW) mutation calling pipeline as part of "Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates."
Most of this pipeline is in the R coding language, but also makes use of bash commands and the 'bcftools' utility. Some bash commands are also interspersed in the .R scripts, these are commented out and begin with a $.
Not included with these scripts are the large alignment (.bam) and variant call (.vcf) files.