bammix
Project description
bammix
Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures
Usage
usage: bammix -b bam_file.bam -p positions [options]
bammix
optional arguments:
-h, --help show this help message and exit
-b BAM, --bam BAM BAM file to be examined
-p POSITIONS [POSITIONS ...], --positions POSITIONS [POSITIONS ...]
Set of positions to be checked
-r REFERENCE, --reference REFERENCE
Name of reference the reads were mapped against, default MN908947.3
-q BASE_QUALITY, --base_quality BASE_QUALITY
Minimum base quality to include a base in counts, default is to include all bases regardless of quality
-m MAPPING_QUALITY, --mapping_quality MAPPING_QUALITY
Minimum mapping quality to include a read in counts, default is to include all reads
-o O Optional prefix for output files, default is no prefix
Install
pip install bammix
Project details
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