Skip to content

Compute coverage QC

Compute coverage QC metrics over regions in the panel

computeCoverageQC

Compute coverageQC metrics across panel regions.

Usage:

computeCoverageQC [OPTIONS]

Options:

Name Type Description Default
--panelPosFile Path File with panel positions as generated by buildIndex command.File should have six columns: Chr.Pos, Chr, Start, End, Gene, RegionLength _required
--summaryPosFile Path File with unique positions in the panel to compute sample level summary statistics. File should have one column: Chr.Pos, as generated by buildIndex command. _required
--countFile Path Count file(s) generated by SequencErr program. File(s) should've seven columns: Chr, Pos, A_Q_30, C_Q_30, G_Q_30, T_Q_30, N_Q_30 _required
--outdir Path Output directory path. None
--outSummary / --no-outSummary boolean Output counts at summary positions False
--help boolean Show this message and exit. False

How to generate count files?

The count files should be generated using SequencErr1

Please refer to Generating count files

Output files
  • computeCoverageQC generates two output files.
  • Panel_regionQC file
    • This file consists of the region level QC metrics for all the regions in the panel
  • Sample_summaryQC file
      • This file consists sample level QC metrics across all the positions in the panel
Output format
Panel_regionQC file
Chr Start End Gene RegionLength paddedLength Mean SD basecount_2SD basecount_1.5SD basecount_1SD
chr1 1718760 1718886 GNB1 127 127 32883.11 3783.5 127 127 127
chr1 1720482 1720718 GNB1 237 237 30500.3 4670.12 237 237 237
. . . . . . . . . . .
. . . . . . . . . . .
chrX 153629033 153629205 RPL10 173 173 17666.45 2345.65 173 173 166
chrX 153711341 153711341 chrX.153711341.C.G 1 1 25764.0 1 1 1
Sample_summaryQC file
Sample sampleMean sampleMedian sampleSD CV cut_2SD cut_1pt5SD cut_1SD quantile_20 fold_80 uniformityOfCoverage Pcntbase_2SDPcntbase_1.5SD Pcntbase_1SD
EW-8_S5 21974.68 20209.0 14067.16 0.64 -6159.64 873.94 7907.52 12573.0 1.75 94.92 100.0 98.37

  1. Davis, E.M., Sun, Y., Liu, Y., Kolekar, P. et al. SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data. Genome Biol 22, 37 (2021). https://doi.org/10.1186/s13059-020-02254-2 ↩