Output from the Identify Known Variants in One Sample (WES)

The Identify Known Variants in One Sample (WES) tool produces five different output types:

It is a good idea to start looking at the Target Regions Coverage Report to see whether the coverage is sufficient in the regions of interest (e.g. > 30 ). Please also check that at least 90% of the reads are mapped to the human reference sequence. In case of a targeted experiment, we also recommend that you check that the majority of the reads are mapping to the targeted region.

When you have inspected the target regions coverage report you can open the Genome Browser View Identify Known Variants file (see 16.13).

The Genome Browser View includes an overview track of the known variants and a detailed result track presented in the context of the human reference sequence, genes, transcripts, coding regions, targeted regions, and mapped sequencing reads.

Image identify_known_variants_in_one_sample_result1_wes
Figure 16.13: Genome Browser View that allows inspection of the identified variants in the context of the human genome and external databases.

Finally, a track with conservation scores has been added to be able to see the level of nucleotide conservation (from a multiple alignment with many vertebrates) in the region around each variant.

By double clicking on one of the annotated variant tracks in the Genome Browser View, a table will be shown that includes all variants and the added information/annotations (see  16.14).

Image identify_known_variants_in_one_sample_result2_wes
Figure 16.14: Genome Browser View with an open overview variant track with information about if the variant has been detected or not, the identified zygosity, if the coverage was sufficient at this position and the observed allele frequency.

Note We do not recommend that any of the produced files are deleted individually as some of them are linked to other outputs. Please always delete all of them at the same time.