A tool for diagnosing spinal muscular atrophy (SMA) using exome or genome sequencing data
Project description
sma_finder.py: A tool for diagnosing spinal muscular atrophy (SMA) based on exome or genome sequencing data.
Install
python3 -m pip install sma-finder
Usage
usage: sma_finder [-h] -R REFERENCE_FASTA -g {37,38,T2T} [-o OUTPUT_TSV] [-v]
cram_or_bam_path [cram_or_bam_path ...]
positional arguments:
cram_or_bam_path One or more CRAM or BAM file paths
optional arguments:
-h, --help show this help message and exit
-R REFERENCE_FASTA, --reference-fasta REFERENCE_FASTA
Reference genome FASTA file path
-g {37,38,T2T}, --genome-version {37,38,T2T}
Reference genome version
-o OUTPUT_TSV, --output-tsv OUTPUT_TSV
Output tsv file path
-v, --verbose Whether to print extra details during the run
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