Custom - Summary ReportΒΆ

Summarizing key metrics from sequencing (FASTQC), mapping (Qualimap) and variant calling (GATK) in a single report file.

Location

  • Filepath: <SnakeLines_dir>/rules/shared/variant/report/summary/custom.snake
  • Rule name: custom__summary_report

Input(s):

  • fastqc_original: FASTQC report on original reads.
  • fastqc_trimmed: FASTQC report on trimmed reads.
  • qualimap_txt: Plain text Qualimap report on deduplicated mapped reads.
  • qualimap_html: HTML Qualimap report on deduplicated mapped reads.
  • calling_stats: GATK variant calling metrics.

Output(s):

  • xml: Report for further computer processing.
  • html: Formatted report which is used to generate PDF report.
  • pdf: Human readable report in form of PDF document.