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Callstate

A tool that generates similar results as CallableLoci in GATK3 but runs much faster.

Algorithm

This tool uses similar depth calculating algorithm in Mosdepth to calculate the raw depth, qc depth and low_mapq depth and then uses the same algorithm in CallableLoci tool in GATK3 to determine the following callable states:

  • REF_N
  • NO_COVERAGE
  • LOW_COVERAGE
  • POOR_MAPPING_QUALITY
  • EXCESSIVE_COVERAGE
  • CALLABLE

For each region in the output file, besides the location of region, Callstate also outputs the mean raw depth, mean QC depth, and the mean Low MAPQ depth

Usage

callstate 0.0.1

  Usage: callstate [options] <BED> <BAM>

Arguments:

  <BAM>  the alignment file for which to calculate callable states
  <BED>  The BED file that contains regions.

Common Options:

  -t --threads <threads>                 Number of BAM decompression threads [default: 4]
  -o --output <output>                   The output BED file.
  -mbq --min-base-qual <mbq>             The minimum base quality for a base to contribute to QC depth [default: 10]
  -mmq --min-mapq <mmq>                  The minimum mapping quality of reads to count as QC depth [default: 10]
  -mdp --min-depth <mdp>                 The minimum QC read depth before a read is considered callable [default: 20]
  -mlmq --max-low-mapq <mlmq>            The maximum value of MAPQ before a read is considered as problematic mapped read. [default: 1]
  -mxdp --max-depth <mxdp>               The maximum read depth before a locus is considered high coverage [default: -1]
  -mdflmq --min-depth-low-mapq <mdflmq>  Minimum read depth before a locus is considered candidate for poorly mapped [default: 10]
  -frlmq --low-mapq-frac <frlmq>         If the fraction of low mapping reads exceeds this value, the site is considered poorly mapped [default: 0.5]

Other options:

  -F --flag <FLAG >                      exclude reads with any of the bits in FLAG set [default: 1796]
  -h --help                              show help

Examples

To run with default values for all parameters:

callstate -o <output.bed> <capture.bed> <bam/final.bam>

Sample output

#chrom  start   end     call_state      raw_depth       qc_depth        low_mapq_depth
22      17565780        17566404        CALLABLE        309.22  305.61  0.00
22      17577753        17577787        LOW_COVERAGE    10.41   9.76    0.00
22      17577787        17577789        POOR_MAPPING_QUALITY    161.78  31.23   129.76
22      17577789        17577790        LOW_COVERAGE    20.00   19.00   0.00
22      17577790        17578173        CALLABLE        120.22  119.55  0.00