SEQ Help Center

# Advanced Multisample Analysis

# When to use

The Multisample Analysis will enable the cross-comparison of multiple samples, together with population allele frequency and geneset filters. Filtering for a combination of heterozygote, homozygote, wild type, and no-call genotypes in a sample is supported. The multisample analysis is suitable for the de novo variant selection of a trio case where the parents must carry a wild-type genotype, and the child will have to be hom/het depending on the mode of inheritance.

# Starting an analysis

To start the Multisample Analysis, you can either go to the "Samples" page and click the "Add Multisample Analysis" button in the "Multisample Analysis" column or go to the sample dashboard of one of your samples and click on the "Start New Multisample Analysis" option in the menu in the Multisample Analysis card.

Multisample Button
  • Give your analysis a name. Then, select the annotation source (Ensembl or RefSeq) and hit "Continue".
  • Select the samples that will be included in the multisample analysis. You can search for samples in your account by typing the name and selecting the sample from the dropdown menu.
  • Select the relation of the sample in your analysis cohort and click the "Add" button. You can add up to 10 samples.
  • When you add all the samples you want to include in the analysis, hit “Continue".
  • You will see the summary of the analysis. If you confirm, hit the "Confirm" button. If you want to make changes, hit the "Edit" button.

Your analysis will start after your confirmation.

# Results

To access the results of the multisample analysis, either go to the sample page and click on the "Multisample" tab or on the “sample list” click on the "Multisample" button and click on the sample you wish to analyze using the "Samples" button under the "Available Analyses" list.

The multisample analysis interface is the same as the "Variants" interface except for the following:

  • In the "Genotype & Quality" column, you will see the information for all samples included in the analysis.
  • Under the "Filters" menu, you can select the desired genotypes of all your samples to filter for variants with any combination of heterozygous, homozygous, wild type, or no-call among the cohort.

# No-call Variants in Multisample Analysis

If the sequencing information is missing in any of the samples, they will be classified as "no-call" variants and will be shown with a "light gray chromosome" in the "Genotype & Quality" column. This means that either this position is not sequenced in this sample or that reads do not have the required minimum quality values. This information is especially helpful in de-novo analysis when either of the parents has a no-call variant while the other parent is wild-type. In this case, classifying the variant observed in the proband would not be correct since we do not have any information about the genotype of the "no-call" parent.

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