Output formats

Squirls supports storing results in 4 output formats: HTML, VCF CSV, and TSV. Use the -f | --output-format option to select one or more of the desired output formats (e.g. -f html,vcf). HTML report is generated by default.

HTML output format

Squirls creates an HTML file with the analysis summary and with variants sorted by Squirls score in descending order. The number of the reported variants is adjusted by the -n | --n-variants-to-report option. See the Result interpretation section to learn more about the content of the HTML report.

VCF output format

When including vcf into the -f option, a VCF file with all input variants is created. The annotation process adds a novel FILTER and INFO field(s) to each variant that overlaps with one or more transcript region:

• SQUIRLS - a FILTER flag indicating that the variant is considered to have a deleterious effect on >=1 overlapping transcript

• SQUIRLS_SCORE - an INFO string containing maximum SQUIRLS scores for the overlapping transcripts.

• SQUIRLS_TXS - an INFO string containing SQUIRLS scores for each variant-transcript combination. The field is present when --all-transcripts option is specified.

For the example variant chr1:1234C>A,G, the INFO field will contain the following:

SQUIRLS_SCORE=0.988654;SQUIRLS_TXS=A|NM_123456.1=0.988654|ENST00000987654.1=0.988654
SQUIRLS_SCORE=0.330112;SQUIRLS_TXS=G|NM_12356.1=0.330112|ENST00000987654.1=0.330112

Multi-allelic variants are broken down into separate records and processed individually. Predictions with respect to the overlapping transcripts are separated by a pipe (|) symbol.

Note

The -n option has no effect for the VCF output format.

Note

The vcfgz output format has been deprecated. Use --compress and -f vcf options to get results as a compressed VCF file.

CSV/TSV output format

To write n most deleterious variants into a CSV (or TSV) file, use csv (tsv) in the -f option.

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

Tabular output

chrom	pos	ref	alt	gene_symbol	tx_accession	interpretation	squirls_score
chr3	165504107	A	C	BCHE	NM_000055.2	pathogenic	0.99997203304
…	…	…	…	…	…	…	…

Note

Use --report-features and/or --all-transcripts options to add columns with Squirls features and/or Squirls scores for all overlapping transcripts.