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.