Output formats

SvAnna supports storing results in 4 output formats: HTML, VCF CSV, and TSV. Use the --output-format option to select one or more of the desired output formats (e.g. --output-format html,vcf).

HTML output format

SvAnna creates an HTML file with the analysis summary and with variants sorted by the \(PSV\) score in descending order. By default, top 100 variants are included into the report. The number of the reported variants can be adjusted by the --report-top-variants option.

The report consists of several parts:

  • Analysis summary - Details of HPO terms of the proband, paths of the input files, and the analysis parameters.

  • Variant counts - Breakdown of the number of the variant types of the different categories.

  • Prioritized SVs - Visualizations of the prioritized variants.

Note

Only the variants that passed all the filters are visualized in the Prioritized SVs section.

The --no-breakends option excludes breakends/translocations from the report.

VCF output format

When including vcf into the --output-format option, a VCF file with all input variants is created. The prioritization adds a novel INFO field to each variant:

  • PSV - an INFO field containing \(PSV\) score for the variant.

Note

  • --report-top-variants option has no effect for the VCF output format.

  • Add --uncompressed-output flag if you want to get uncompressed VCF file.

CSV/TSV output format

To write the prioritization results into a CSV (or TSV) file, use csv (tsv) in the --output-format option.

The results are written into a tabular file with the following columns:

  • contig - name of the contig/chromosome (e.g. 1, 2, X).

  • start - 0-based start coordinate (excluded) of the variant on positive strand.

  • end - 0-based end coordinate (included) of the variant on positive strand.

  • id - variant ID as it was present in the input VCF file.

  • vtype - variant type, one of {DEL, DUP, INV, INS, BND, CNV}.

  • failed_filters - the names of filters that the variant failed to pass. The names are separated by semicolon (;) * filter - the variant failed previous VCF filters - at least one filter flag is present in the variant VCF line, except for PASS. * coverage - the variant is supported by less reads than specified by --min-read-support option.

  • psv - the \(PSV\) score value.

Tabular output

contig

start

end

id

vtype

failed_filters

psv

11

31130456

31671718

abcd

DEL

109.75766900764305

18

46962113

46969912

efgh

DUP

filter;coverage

3.2

…

…

…

…

…

…

…

Note

  • --report-top-variants option has no effect for the CSV and TSV output formats.

  • Add --uncompressed-output flag if you want to get uncompressed VCF file.