Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures
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, will be extracted from the BAM if not provided
-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 OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
Optional prefix for output files, default is no prefix
pip install bammix