---
# System prepended metadata

title: Input & Outputs

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# Input & Outputs
- Fastqc- Alignment
    - Align with bwamem2 and sentieon
    - Mitochondria
- Call variants
    - SNV
        - Deepvariant
        - Sentieon
    - SV
    - Mitochondria
- Annotation SNV
- Annotation SV
- Annotation mitochondria




### SMNCopyNumberCaller
A tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file. Please refer to https://github.com/Illumina/SMNCopyNumberCaller for the full documentation.

**Input_1:** list of bam/cram files.
**Output_1:** tsv file containing copy numbers and raw normalized read depth for SMN1, SMN2, and SMN2Δ7–8.
**Output_2:** json file useful for debugging purposes.
