broadinstitute/smn_analysis

Code for analyzing SMN1/SMN2

SMN_ANALYSIS Tool

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

Dependencies

• Python3
• Python Libraries
• Pandas
• Matplotlib
• Pysam
• bedtools
• htslib (bgzip & tabix) and samtools
• gcloud
• gsutil
• ...

Installation

Use git to clone the package and install

$ git clone [email protected]:broadinstitute/smn_analysis.git

$ cd smn_analysis/

Usage

$ 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

Output

Based on the -o/--output-tsv parameter, smn_analysis will output a tsv file with unknown, unaffected and affected samples with SMA.

smn_analysis's Issues

smn_analysis.py

@bw2 I made changes to the script. So far it's reading the files separately and creating .tsv file. It still has some issues I need to troubleshoot. It's printing header list every time I run the sample files.