Liatir

Appearance

SnpSift Filter ​

SnpSift Filter keeps only VCF variants that match a rule. SnpSift is included in the same verified, on-demand suite as SnpEff, so there is no second program to download or configure.

Presets ​

The page offers readable presets for:

  • high-impact variants;
  • high- or moderate-impact variants;
  • missense variants;
  • stop-gained variants;
  • a minimum VCF quality score;
  • an advanced SnpSift expression.

The first four read ANN, the annotation field written by SnpEff. If the input VCF has not been annotated, run SnpEff first. The quality preset works on an ordinary VCF.

Liatir always shows and records the exact expression generated by a preset. Advanced expressions are passed as one argument to SnpSift; they are not interpreted by a shell.

Output and memory use ​

The filtered VCF is streamed directly to its result file. Liatir does not load the complete VCF into memory, so large files do not freeze the interface.

Every run records the preset, exact expression, suite version, suite checksum and whether the suite was managed or external.

Pipeline use ​

SnpSift Filter is available as a pipeline node with the same presets and expression rules as the standalone page. A common flow is SnpEff → SnpSift Filter: annotate variants, then keep only the effects relevant to the analysis.