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Build Index

Buid index
Generate index for the panel
DeepSeqCoverageQC buildIndex --help

buildIndex

Generate index for the panel

Usage:

buildIndex [OPTIONS]

Options:

Name Type Description Default
--panelFile Path File with panel regions. File should have four tab-delimited columns: Chr, Start, End, Gene _required
--outfile Path Output file name. None
--padding integer Padding (bp) for regions. 0
--chr / --no-chr boolean Add 'chr' prefix False
--help boolean Show this message and exit. False
Input file format for --panelFile
Chr Start End Gene
chr1 998582 998582 chr1.998582.G.C
chr1 1098421 1098421 chr1.1098421.C.T
chr1 1646371 1646371 chr1.1646371.G.T
chr1 1718760 1718886 GNB1
chr1 1720482 1720718 GNB1
Output files
  • buildIndex generates two output files.
  • *_regions.txt file
    • This file consists of expanded panel region positions retaining gene and length information
    • This file is used to calculate region level QC metrics using computeCoverageQC
  • *_uniquePositions.txt file
    • This file consists of unique positions in the panel to calculate sample level QC metrics using computeCoverageQC
Output format
*_regions.txt file (partial output)

Note

Please note that original region chr1:1718760-1718886 is being expanded over individual positions as shown under Chr.Pos column

Chr.Pos Chr Start End Gene RegionLength
chr1.1718760 chr1 1718760 1718886 GNB1 127
chr1.1718761 chr1 1718760 1718886 GNB1 127
chr1.1718762 chr1 1718760 1718886 GNB1 127
chr1.1718763 chr1 1718760 1718886 GNB1 127
*_uniquePositions.txt file (partial output)
Chr.Pos
chr1.100345409
chr1.100939777
chr1.101106981
chr1.101750747
chr1.102322817