SMNCopyNumberCaller is a tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN* (SMN1/2Δ7–8, with a deletion of Exon7-8) from a WGS bam file. Please refer to our medRxiv link for details about the method.
SMNCopyNumberCaller is provided under the terms and conditions of the Apache License Version 2.0. It requires several third party packages (numpy, scipy, statsmodels and pysam) provided under other open source licenses, which are listed in COPYRIGHT.txt.
This Python3 program can be run as follows:
./smn_caller.py --manifest MANIFEST_FILE \
--genome [19/37/38] \
--prefix OUTPUT_FILE_PREFIX \
--outDir OUTPUT_DIRECTORY \
--threads NUMBER_THREADSEach line in the manifest file should list the absolute path to an input bam file.
The program produces a .tsv file in the directory specified by --outDir.
The fields are explained below:
| Fields in tsv | Explanation |
|---|---|
| Sample | Sample name |
| isSMA | Whether sample is called as SMA (zero copy of SMN1) |
| isCarrier | Whether sample is called as SMA carrier (one copy of SMN1) |
| SMN1_CN | Copy number of SMN1 (None means no-call) |
| SMN2_CN | Copy number of SMN2 |
| SMN*_CN | Copy number of SMN* (with deletion of Exon7-8) |
| Total_CN_raw | Raw normalized depth of total SMN |
| Full_length_CN_raw | Raw normalized depth of full-length SMN |
| g.27134T>G_CN | CN of g.27134T>G, SNP associated with 2+0 silent carrier |
| SMN1_CN_raw | Raw SMN1 CN values at SNP sites that differ btn SMN1/SMN2 |
A .json file is also produced that contains more information for debugging purpose.
| Fields in json | Explanation |
|---|---|
| Coverage_MAD | Median absolute deviation of depth, measure of sample quality |
| SMN1_read_support | Number of reads carrying SMN1 allele |
| SMN2_read_support | Number of reads carrying SMN2 allele |
| SMN1_fraction | Fraction of reads carrying SMN1 allele |
| g27134TG_REF_count | Number of reads carrying g.27134T |
| g27134TG_ALT_count | Number of reads carrying g.27134G |
| g27134TG_raw | Raw CN value of g.27134T>G |
| Info | Filter value for SMN1 CN call |
| Confidence | Confidence of SMN1 CN calls at SNP sites |