Comparison of track comparison tools

This section of the manual provides an overview about comparison, filtering and annotation tools that work with tracks.

Tool name Description of the tool Example of possible applications Comments
Compare Samples within Group (see Compare Variants within Group) Identifies common variants in a group of samples Identification of common variants in inherited deafness Can also be used to get all variants in a group of samples by setting the frequency threshold to 0%
TRIO analysis (see TRIO analysis) Identifies de novo and accumulated variants in a child by comparing with the variants present in the mother and father Identification of causative variants in rare mendelian diseases -
Fisher Exact Test (see Fisher Exact Test) Identifies enriched variants in a group of samples with a certain phenotype (the case group) in comparison to a group of samples not showing this phenotype (the control group). Control and case samples are from different individuals Identification of causative common variants in non-rare diseases To retrieve significant results, a large number of samples is required for each group

Tool name Description of the tool Example applications Comments
Filter Against Control Reads (see Filter Against Control Reads) Removes germline variants from a set of called variants in a case sample (e.g. a cancer sample) by using mapped sequencing reads from a normal sample from the same individual Comparison of cancer versus normal from the same patient -
Filter against known variants (see Filter against known variants) Removes variants that are present (or absent) in an external variant database (available as track) from a set of called variants Removal of common (assumed germline) variants from a set of called variants in a case sample to identify somatic variants -
Annotate against known variants (see Annotate against known variants) Adds information from one or several external database(s), that are available as track(s), to called variants in a sample to see how many of them are known in this(these) database(s) Adds information from COSMIC to see how many of the variants found in the sample are known to be associated with cancer The tool has special rules for when information from the database are transferred and when it is not. This means that only information is transferred in cases with exact matches (when the same variant is found in the sample AND the database) and in cases where variants in the database are completely contained in the set of variants that have been called in the sample
Filter based on overlap (see Filter based on overlap) Removes elements from a set of genetic annotations such as genes, regulatory elements, or variants. Only genetic annotations are kept that overlap or do not overlap regions in the other track Removing deletions or amplifications that do not overlap genes to identify those that are potential causative. Filtering away variants outside targeted regions in an DNA amplification sequencing experiment -
Compare Sample Variant Tracks (see Compare Sample Variant Tracks) Removes variants called in one sample that are also called (or not called) in another sample for comparison Sample/normal comparison Please note that this tool has the same functionality as the Annotate against known variants tool, but should be used for called variants only and not for comparison or filtering using databases