Is it possible to reduce the variant fraction limit to 0.1% (or 0.5%) to find very low frequency somatic mutations?
Yes, the custom filter builder can be used to find variants with low variant fractions. For detailed instructions please refer to the Operation Manual Section 5. Alternatively follow these simplified instructions:
1) New filters use only retained variants by default. Low confidence variants can be added by dragging the built-in rule “Low confidence” onto the left bar with the initial variants count. This ensures your new filter contains both retained and the low-confidence variants.
2) Create a filter for the low-confidence variants based on the filter value. Select “Filter” from the drop down box on the top right corner and drag it onto the “”low confidence variants”” box. By selecting this feature the filter value should be “low_variant_fraction”, and as a result, only low-confidence variants that were previously rejected for low variant fraction will now be kept.
3) This filter may be further adapted to include other parameters such as applicability to only variants in certain genes, of certain coding consequences, etc..