SMA Calling With ExpansionHunter

SMA calling is implemented together with repeat expansion detection using sequence-graph realignment to align reads to a single reference that represents SMN1 and SMN2.

In addition to the standard diploid genotype call, SMA Calling with ExpansionHunter uses a direct statistical test to check for presence of any C allele. If a C allele is not detected, the sample is called affected, otherwise unaffected.

SMA calling is only supported for human whole-genome sequencing with PCR-free libraries.

To enable SMA calling along with repeat expansion detection, set the --repeat-genotype-enable option to true. For information on graph-alignment options, see Repeat Expansion Detection with ExpansionHunter.

To activate SMA calling, the variant specification catalog file must include a description of the targeted SMN1/SMN2 variant. The /opt/edico/repeat-specs/experimental folder contains example files.

The <outputPrefix>.repeat.vcf file includes SMN output along with any targeted repeats. SMN output is represented as a single SNV call at the splice-affecting position in SMN1 with SMA status in the following custom fields.

SMA Results in repeat.vcf Output File

Field	Description
VARID	SMN marks the SMN call.
GT	Genotype call at this position using a normal (diploid) genotype model.
DST	SMA status call: + indicates detected - indicates undetected ? indicates undetermined
AD	Total read counts that support the C and T allele.
RPL	Log10 likelihood ratio between the unaffected and affected models. Positive scores indicate the unaffected model is more likely.