Table 1.
SVAFotate Parameters and Options
| Required SVAFotate parameters | Argument | Description | |
|---|---|---|---|
| Input VCF | − v | The input VCF to be annotated by SVAFotate | |
| Input BED | − b | The input BED of reported SVs to use for annotations | |
| Output VCF | − 0 | The name for the resulting, SVAFotate annotated VCF | |
| Optional SVAFotate parameters | Argument | Description | |
|---|---|---|---|
| Reciprocal overlap | − f | The minimum amount of reciprocal overlap required for the matching of SVs (recommended 0.8 or higher) | |
| Extra annotations | − a | Adds annotations corresponding to all extra annotations (best, full, mf, mis, pops) | |
| all: Adds all available information from the BED file for all matches | |||
| best: adds the "best" match for each including source from the BED file | |||
| mf: adds male and female specific data | |||
| mis: Adds "mismatches" for matches with differing SVTYPEs | |||
| pop: Adds populations specific (AFR, AMR, EAS, EUR, OTH, and SAS) data, if available | |||
| Observed SV coverage | − c | Creates annotation reflecting the amount of a given SV in the input VCF has been observed with the same SVTYPE from SVs in the BED file | |
| Unique SV regions | − u | Creates additional output file containing "unique" regions of a given SV that are not obersved to have any overlaps with SVs in the BED file | |
| SV size limit | − l | Maximize size of SVs from the BED file to include alongside − c and − u parameters (recommended 1,000,000) | |
| Targets BED file | − t | Identify overlaps with particular regions of interest reported in an additional BED file | |
| Sources to annotate | − s | Restrict matching of SVs to only those from specified sources in the BED file | |
| Use CI boundaries | − ci | Adjust the genomic breakpoints in the input VCF by the reported inner or outer confidence intervals (CIP0S, CIEND) | |
| − ci95 | Adjust the genomic breakpoints in the input VCF by the reported 95% inner or outer confidence intervals (CIPOS95, CIEN D95) | ||
| Change SV size | − e | Increase the size of the genomic breakpoints in the input VCF | |
| − r | Reduce the size of the genomic breakpoints in the input VCF | ||
| Output file type | − 0 | Specify the output file type as VCF (vcf), compressed VCF (vcfgz), BCF (bcf), or compressed BCF (bcfgz) | |
| CPU count | − cpu | The number of CPUs to use for multi-threading | |
Required SVAFotate parameters are listed followed by optional SVAFotate parameters with all arguments and descriptions for each option included. Recommended optional parameters are listed in italics with accompanying recommendations, as applicable. For full descriptions and details, please refer to the SVAFotate repo: https://github.com/fakedrtom/SVAFotate