Identify Known Mutations from Sample Mappings
The Identify Known Mutations from Sample Mappings tool can be used to look up known genomic variants in read mappings. This can be done in one or more samples by comparing a track of known variants with the read mappings of interest .
The Identify Known Mutations from Sample Mappings tool does not perform any kind of variant calling, which means that this tool cannot be used to find de novo variants. Rather, the tool is intended for identification of variants that have already been reported.
You need two types of input for the Identify Known Mutations from Sample Mappings tool:
- A variant track that holds the specific variants that you wish to test for.
- The read mapping(s) that you wish to check for the presence (or absence) of specific variants.
The Identify Known Mutations from Sample Mappings tool has two kinds of outputs:
- An overview track with information about:
- whether the variant could be detected or not
- whether the coverage was sufficient at the given position
- the frequency of the variant in each sample.
- Individual output tracks for each sample that show the observed frequency, average base quality, forward/reverse read balance, zygosity and observed allele count.
Subsections
- How to run the Identify Known Mutations from Sample Mappings tool
- Output from the Identify Known Mutations from Sample Mappings tool