smn_analysis is a tool to detect Survival Motor Neuron (SMN) mutations to diagnose Spinal Muscular Atrophy (SMA) by counting the total number of reads and the number of C reads at c.840 position in exon 7. This tool also works for
- Python3
- Python Libraries
- Pandas
- Matplotlib
- Pysam
- bedtools
- htslib (bgzip & tabix) and samtools
- gcloud
- gsutil
- ...
Use git to clone the package and install
$ git clone git@github.com:broadinstitute/smn_analysis.git
$ cd smn_analysis/
$ python3 smn_analysis.py -R --reference-fasta -o --output-tsv -v --verbose cram_paths
Example:
$ python3 smn_analysis_C.py -R /Users/r/SMA.2022/Homo_sapiens_assembly38.fasta -o c.tsv -v ../MAAC002.cram
Based on the -o/--output-tsv parameter, smn_analysis will output a tsv file with unknown, unaffected and affected samples with SMA.