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:* /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:* /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:* /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