Qualimap - Mapping Quality Report Across Reference¶
Generate summary statistics for mapped reads stored in BAM files. Statistics are calculated across whole reference genome.
Location
- Filepath: <SnakeLines_dir>/rules/shared/mapping/report/quality_report/qualimap.snake
- Rule name: qualimap__mapping_quality_report_across_reference
Input(s):
- bam: Mapped reads in bam format
- bai: Index to mapped reads for enable fast read retrieval from desired genomic region
Output(s):
- html: Quality report of mapped reads in HTML format
- pdf: Quality report of mapped reads in PDF format
- text: Quality report of mapped reads in format suitable for automated processing
Qualimap - Mapping Quality Report Across Panel¶
Generate summary statistics for mapped reads stored in BAM files. Statistics are calculated across genomic regions specified in the BED file.
Location
- Filepath: <SnakeLines_dir>/rules/shared/mapping/report/quality_report/qualimap.snake
- Rule name: qualimap__mapping_quality_report_across_panel
Input(s):
- bam: Mapped reads in bam format
- bai: Index to mapped reads for enable fast read retrieval from desired genomic region
- bed: Genomic regions of interest in bed format
Output(s):
- html: Quality report of mapped reads in HTML format
- pdf: Quality report of mapped reads in PDF format
- text: Quality report of mapped reads in format suitable for automated processing
Qualimap - Summarize Quality Reports¶
Aggregate results from individual bamqc results to a single summary report
Location
- Filepath: <SnakeLines_dir>/rules/shared/mapping/report/quality_report/qualimap.snake
- Rule name: qualimap__summarize_quality_reports
Input(s):
- reports: List of pdf qualimap reports to aggregate
Output(s):
- html: Aggregated quality report of mapped reads in HTML format
- pdf: Aggregated quality report of mapped reads in PDF format