Karyotyping using low coverage whole genome sequencing.
This pipeline utilises BWA (http://bio-bwa.sourceforge.net/) to map short paired-end sequencing data to a genome sequence to determine a sample's karyotpye. After postprocessing with samtools (http://samtools.sourceforge.net/), the data is further analysed using the QDNAseq R package (https://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html).
The input data should be trimmed, e.g. using TrimGalore or any other comparable quality trimming tool. Unpaired reads resulting from this should be retained and concatenated into one additional read file, e.g. <sample_name>_unpaired.fastq.gz.