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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.