Detect QIAseq Human Identity SNPs and Microhaplotypes (beta)
The workflow Detect QIAseq Human Identity SNPs and Microhaplotypes (beta) can both be used to analyse data from SNP and microhaplotype panels. The default parameter values are set for mixed-sample analysis with sensitivity that allows detection of a human genome present in 10% of the reads.
Note:
- In order to detect alleles present in 5% of the reads, the read coverage of the locus must be at least 200.
- There is not yet any special homopolymer handling, so length variation artifacts must be considered when analysing loci around longer homopolymers.
The Detect QIAseq Human Identity SNPs and Microhaplotypes (beta) template workflow can be found in the Toolbox:
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq DNA Workflows (
) | Detect QIAseq Human Identity SNPs and Microhaplotypes (beta) (
)
Primers, target regions and marker regions for QIAseq Human Identity panels are available in the reference data set QIAseq Human Identity Panels hg19. The reference data can be downloaded via the Reference Data Manager. Alternatively, if you have not downloaded the reference data set before starting the workflow, a dialog will suggest the relevant data set and offer the opportunity to download it using the Download to Workbench button.
If running the workflow with a custom panel, note that primers must be imported into the workbench using Import Primer Pairs (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Import_Primer_Pairs.html).
The following parameters can be adjusted when running the workflow:
- Minimum group size
- Increase to disregard UMI reads with low number of supporting reads.
- Minimum average quality score
- Increase to disregard UMI reads with low quality.
- Maximum phasing distance
- The default value is set for microhaplotypes. It can be set to 1 when analysing SNP panels where marker loci are close to each other, and phasing is not of interest. This may for example be useful when analysing data from the Ancestry and VISAGE SNP panels. Reducing this value may decrease processing time.
- Minimum count (call)
- Read support threshold for called alleles. Alleles with fewer supporting reads can be inspected by enabling 'Show filtered' in the side panels.
- Minimum allele fraction (call)
- Allele fraction threshold for called alleles. Increase this parameter (e.g. to 0.15) to remove noise when the sample only contains the genome of a single individual.
- Minimum haplotype quality (call)
- Quality threshold for called haplotype alleles. Haplotypes with lower quality can be inspected by enabling 'Show filtered' in the side panels.
- Minimum coverage
- Loci with lower coverage are marked as filtered and can be inspected by enabling 'Show filtered' in the side panels.
- Minimum average base quality
- Apply a filter to an allele when UMI read bases supporting the allele have lower average quality than this threshold.