from /fh/fast/ha_g/user/tpersse/pipelines/admixtureAlnSumMetrics

[caalo]

Tracking changes made to the pipeline from Thomas' departure. Full documentation here.

Some slight modifications were made to the original version of the pipeline that were necessitated by multiple input reference genomes. I added three steps to the pipeline, just after remvoeDuplicates and before createCODRmetrics (mixarray_p1.snakefile lines 86-121). The purpose of these steps is to replace all bam headers with versions that have a standardized set of contigs, such that downstream steps can all work seamlessly regardless of which version of hg38 was used in alignment.