ComputeReadDepthCoverage

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin
edited September 2012 in GenomeSTRiP Documentation

1. Introduction

The ComputeReadDepthCoverage walker traverses a set of BAM files to generate
genome-wide read depth statistics.

The read depth coverage is the number of fragments confidently aligning to the
genome (or interval if an interval subset is used). The read depth coverage is
measured only at confidently alignable bases (based on the genome mask) and
only using reads passing the mapping quality filter. Reads are counted as
aligning at the middle aligned base. Sequenced molecules are counted only
once: for paired-end data, only the leftmost end of the pair (the end with the
lowest reference coordinate) is counted.

Read depth coverage is computed and reported for each readgroup, but the
output is keyed by sample and library to allow easy roll up.

See also MergeReadDepthCoverage.

2. Inputs / Arguments

  • -I <bam-file> : The set of input BAM files.

  • -minMapQ <quality-threshold> : Reads below this mapping quality are not
    counted.

  • -excludedReadGroups <file> : Optional file containing a list of read
    groups to ignore (one read group per line).

  • -genomeMaskFile <mask-file> : Mask file that describes the alignability of
    the reference sequence. : See Genome Mask Files.

3. Outputs

  • -O <coverage-file> : Tab delimited output file (default is stdout).
Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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