Alignment

The steps are executed via the pipeline Poppy GMS. For each sample, they consist in: * aligning the reads with BWA-mem, * splitting the alignments per chromosome for better computational performance in downstream processing, * marking the duplicate reads, * merging the per-chromosome aligned files into a single BAM file.

Implementation

See the alignment hydra-genetics module documentation for more details on the softwares that are used to trim and merge the reads. Default hydra-genetics settings/resources are used if no configuration is specified.

Software versions

See what containers are specified in the config YAML file of Poppy GMS, which are possibly overwritten and/or complemented by containers in poppy-uppsala.