Variant tracks
A variant track created with the variant callers in CLC Genomics Workbench (see Quality-based variant detection and Probabilistic variant detection) has the following information for each variant:
- Information about location, etc
- This is all basic information to locate the variant. Furthermore there is information about the reference sequence at the variant position.
- Variant type
- This can either be SNV (single-nucleotide variant), insertion, deletion or replacement. Learn more in Variant types.
- Allele
- This is the allele found by the variant caller in the sequencing data. In the case where a heterozygous variant is found, there is an entry for each allele, also if one is the reference allele.
- Count
- The number of reads supporting the allele.
- Coverage
- The general read coverage at this position. (See also more information about Detailed information about overlapping paired reads.)
- Frequency
- The number of reads supporting the allele divided by the number of overall reads. See Remove marginal variant calls on how to remove variants that are low-frequency.
- Forward read count
- The number of forward reads supporting the allele. (See also more information about Detailed information about overlapping paired reads.)
- Reverse read count
- The number of reverse reads supporting the allele. (See also more information about Detailed information about overlapping paired reads.)
- Forward/reverse balance
- Some systematic sequencing errors can be triggered by a certain combination of bases. This means that sequencing one strand may lead to sequencing errors that are not seen when sequencing the other strand (see [Nguyen et al., 2011] for a recent study with Illumina data).In order to evaluate whether the distribution of forward and reverse reads is approximately random, this value is calculated as the minimum of the number of forward reads divided by the total number of reads and the number of reverse reads divided by the total number of reads supporting the variant. An equal distribution of forward and reverse reads for a given allele would give a value of 0.5. See Remove marginal variant calls on how to remove variants that score poorly on the read balance. (See also more information about Detailed information about overlapping paired reads.)
- Average quality
- The average read quality score of the bases supporting a variant. See Remove marginal variant calls on how to remove variants that have a low average quality. If there are no values in this column, it is probably because the sequencing data was imported without quality scores (learn more about importing quality scores from different sequencing platforms in Import high-throughput sequencing data). For deletions, the quality scores of the two surrounding bases are taken into account, and the lowest value of these two is reported.
Please note that the information above can be enriched using the annotation tools in Filtering and annotating variants.
A variant track can be exported in VCF or GVF formats. Please note that in order to export to VCF, you have to select both a variant track and a corresponding reference sequence track before clicking Export (
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