Command Line Help

usage: kbbq [-h] [-v] {recalibrate,benchmark,plot} ...

K-mer Based Base Quality score recalibration

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

command:
  valid commands

  {recalibrate,benchmark,plot}

recalibrate

Warning

Recalibrating reads from a BAM file is not yet supported. Use the samtools fastq command to convert your reads to fastq format. This should go something like:

samtools sort -n -O bam input.bam > namesorted.bam
samtools fastq -t -N -F 3844 -O -0 /dev/null -s /dev/null -1 reads.1.fq -2 reads.2.fq namesorted.bam

Reads must then be interleaved for input. This can be done with a tool like seqtk:

seqtk mergepe reads.1.fq reads.2.fq > reads.merged.fq

See FASTQ Input Help for more information.

usage: kbbq recalibrate [-h] (-b BAM | -f FASTQ FASTQ) [-u] [-s]
                        [-g GATKREPORT] [--infer-rg]

Recalibrate a BAM or FASTQ file

optional arguments:
  -h, --help            show this help message and exit
  -b BAM, --bam BAM     BAM to recalibrate
  -f FASTQ FASTQ, --fastq FASTQ FASTQ
                        FASTQ file to recalibrate and a corrected version from
                        your favorite error corrector.
  -u, --use-oq          Use the OQ tag to get quality scores when working with
                        a BAM file. Does nothing if a fastq file is provided.
  -s, --set-oq          Set the 'OQ' flag prior to recalibration. Only works
                        when producing BAM output.
  -g GATKREPORT, --gatkreport GATKREPORT
                        If the given path points to an existing GATK report,
                        load the model from the report instead of calculating
                        it. If the file doesn't exist, save the calculated
                        model to the given path.
  --infer-rg            Attempt to infer the read group from a FASTQ read.
                        Only works with FASTQ input. The default behavior is
                        to treat each input FASTQ file as its own read group.

benchmark

usage: kbbq benchmark [-h] -b BAM -r REFERENCE -v VCF [-f FASTQ] [-l LABEL]
                      [-u] [-d BEDFILE]

Benchmark a BAM or FASTQ file using a truth set

optional arguments:
  -h, --help            show this help message and exit
  -f FASTQ, --fastq FASTQ
                        fastq file to benchmark
  -l LABEL, --label LABEL
                        label to use for label column
  -u, --use-oq          Use the OQ tag to get quality scores when working with
                        a BAM file. Does nothing if a fastq file is provided.
  -d BEDFILE, --bedfile BEDFILE
                        BED file of confident regions. Sites outside the given
                        regions will be skipped.

required arguments:
  -b BAM, --bam BAM     Truth set BAM file. Differences from the reference at
                        nonvariable sites will be interpreted as errors.
  -r REFERENCE, --reference REFERENCE
                        FASTA file containing the reference genome
  -v VCF, --vcf VCF     VCF file containing variable sites

plot

usage: kbbq plot [-h] [-t {calibration,sample-size}] -o OUTFILE [file]

Plot data output from the benchmark command

positional arguments:
  file                  Input file

optional arguments:
  -h, --help            show this help message and exit
  -t {calibration,sample-size}, --type {calibration,sample-size}
                        Type of plot to produce

required arguments:
  -o OUTFILE, --outfile OUTFILE
                        file name to save plot as