Output Hierarchy

ScaleHD’s output is fairly straightforward. For each job that you run, there will be one master output folder containing all data produced by the pipeline. If the user specified a ‘-j’ argument in the command line interface, the output folder will be named as such; if not, the folder will be named ScaleHD-DateTime.

Within the master folder, there will be a few instance-wide report files:

  • AlignedDistributions.csv
  • InstanceGraphs.pdf
  • InstanceReport.csv
  • UtilisedConfiguration.xml

AlignedDistributions contains a matrix of read count distributions for each allele, in each sample processed by the pipeline. Each individual allele’s distribution will be aligned to the same index within this matrix; the peak, or n-value, of each allele is at the same index. This allows the user an easy method by which to cross-compare levels of somatic mosaicism.

InstanceGraphs is a series of graphs rendered for each sample. These graphs plot the CCG distribution, and respective CAG distributions for each allele in a sample. This allows the user to easily search for samples that may require manual inspection and view read count distributions quickly.

InstanceReport is the ‘main’ report output from ScaleHD, and displays allele genotypes and relevant statistics, data characteristics and errors (where applicable). A detailed explanation of what each of the attributes/flags in this file explains, please see Miscellanious Definitions.

UtilisedConfiguration is a literal copy of the ScaleHD configuration file specified as input by the user when the job was launched.

In addition to this, each stage of the ScaleHD pipeline will have a respective output folder with relevant data within:

  • SeqQC – containing FastQC reports and any trimming reports
  • Align – containing aligned reads (in *.SAM format), an alignment report and alignment statistics. These files are present for both FW and RV data.
  • Predict – containing a genotype graph PDF, reports on each allele’s genotype (and associated flags), as well as a penalties log for each allele (stating what was deducted from each allele during confidence calculation). Variant calls are also present in this folder, with a VCF file from Freebayes available for further analysis. However, if variants were detected in contigs which are not either of the alleles in a sample, these ‘irrelevant’ variants are reported on in their own report file.

HTML based output

As of version 0.321, ScaleHD renders HTML output that provides an easy-to-share summary of all samples processed within a run of ScaleHD. We utilise Gridism, JQuery, Chart.js (and extensions), and MSAViewer to render all aspects of ScaleHD output within the browser, minimising file size. Proper write-up documentation of this will come for version 0.322, which will have additional features added to the webpage output.