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Python Perl Makefile
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usage: simple-consensus-per-read-group [-h] [-t x] [-d n] [--max-depth n] [-a] [--ignore-read-groups] [--missing-quality q] input.bam Constructs a simple (dumb) consensus sequence for each read group (RG) in a BAM file. Base qualities are averaged for each site. Percent identity thresholding is done to call a consensus base. If no base reaches the threshold, an N is called. Consensus sequences span only the reference bases between the first and last covered base. Multiple reference sequences (such as chromosomes or contigs) will get separate consensus sequences. Input must be a BAM file indexed with `samtools index`. Output is FastQ. positional arguments: input.bam SAM/BAM file of aligned reads optional arguments: -h, --help show this help message and exit -t x, --threshold x Frequency threshold below which a base is not called (default: 0.7) -d n, --min-depth n Read depth below which a base is not called (default: 1) --max-depth n Maximum number of reads considered for a single consensus position (default: 8000) -a, --ambiguous Call bases below threshold with ambiguity codes (default: False) --ignore-read-groups Ignore read groups and lump all reads into one consensus (default: False) --missing-quality q Quality score to use for bases missing a quality score (default: 0) version 1.2.2 Copyright 2015–2018 by Thomas Sibley <firstname.lastname@example.org> Mullins Lab <https://mullinslab.microbiol.washington.edu> Department of Microbiology University of Washington