Coverage Summary¶
Command examples:¶
atav.sh --coverage-summary --sample PATH_TO_SAMPLE_FILE --gene-boundary PATH_TO_GENE_BOUNDARY_FILE --min-coverage 10 --out PATH_TO_OUTPUT_DIR
Command options:¶
--coverage-summary: trigger coverage summary function.
--percent-region-covered: Specify a number between 0 and 1 (default to 0). When a sample has less than this percent of the region covered, the region will not be considered covered.
Output:¶
coverage.details.by.exon.csv: This file provides more detailed coverage information at the (sample, region, exon) level for input gene/transcript.
- Sample: The sample name extracted from the input sample file.
- Gene: The gene name extracted from the input gene boundary file.
- Chr
- Exon: The particular exon stable_id used for calculation.
- Start_Position
- Stop_Position
- Length: The total number of bases from a particular exon from given gene/transcript.
- Covered_Base: The total number of qualifying covered bases from AnnoDB for the given sample, gene/transcript and exon.
- %Bases_Covered: This is the percent of bases that are covered (Covered_Bases/Length).
- Coverage_Status: This is a Pass/Fail indicator for %Bases_Covered based on command option --percent-region-covered.
sample.summary.csv: This file outputs the summary coverage information for each sample from the sample file.
- Sample: The sample name extracted from the input sample file.
- Total_Bases: The total number of bases from all given regions queried.
- Total_Covered_Bases: The total number of qualifying covered bases from AnnoDB for the given sample.
- %Overall_Bases_Covered: This is the percent of bases that are covered (Total_Covered_Bases/Total_Bases).
- Total_Regions: Total number of input regions that are successfully mapped onto ensembl core database.
- Total_Covered_Regions: : Total number of regions that pass the --percent-region-covered cutoff.
- %Regions_Covered: This is the percent of regions that are covered(Total_Covered_Regions/Regions_Covered).
coverage.details.csv: This file provides detailed coverage information for each (sample, region queried) pair.
- Sample: The sample name extracted from the input sample file.
- Gene: The gene name extracted from the input gene boundary file.
- Chr
- Length: The total number of bases from the given region.
- Covered_Base: The total number of qualifying covered bases from AnnoDB for the given sample and the given region.
- %Bases_Covered: This is the percent of bases that are covered (Covered_Bases/Length).
- Coverage_Status: This is a Pass/Fail indicator for %Bases_Covered based on command option --percent-region-covered.