GeneTalk now helps you when you have a bunch that have to be filtered with the same filter settings. We added two features for supporting such batch processing:

• You can upload a ZIP-file containing serveral VCF files. GeneTalk will unpack your ZIP-file and add all VCF files to your account
• When selecting an individual for filtering, you can now select several individuals (even from different VCF files) that are all filtered with the same filter settings. Of course, filtering several individuals separately will be performed in background; you will get a notification when a file is filtered. You can specify three placeholders for the output of the filtering process:
  • ‘*’ will be replaced by the name of the input file
  • ‘%’ will be replaced by the identifier of the individual
  • ‘#’ will be replaced by the by a consecutive number (this will be handy if all your individuals are located in the same input file and share the same identifier)

  Batch processing is not to be confused with segregation filtering (i.e., filtering several individuals as a “collection”): While the former filters each individual separately allowing, for example, filtering for homozygeous positions, the latter can apply filters that affect every individual in the collection such as the compound heterozygeous filter.

GeneTalk now supports coupled filtering of two or more individuals!

The first step is to create a new VCF file that contains all the individuals or, if you already uploaded a such a file, enter the phenotype information for your file.
You can create a file with multiple individuals by using the new function “Create Collection” in the “Manage Files” menu (sorry for the plain table-based editor, we are working on a graphical editor for this).

To edit phenotype information for an existing file, click the pedigree-tree-shaped icon behind the VCF file in the list of your VCF files (“Manage Files”, “List”).

Once you have a file with phenotype information, the file will be shown in the “Select VCF” tab on the “Filter VCF” page under “Collections”. You will find the choices for segregation filtering in the “inheritance mode” tab, after you selected a file with phenotype information.

The segregation filter allows you to focus on variants that fit to a certain segregation pattern with respect to the phenotype that you are analyzing.

• If you are analyzing a disease where the phenotype seems to follow a recessive pattern of inheritance (typical scenario: in a large pedigree: Around one out of four offsprings are affected by the disease and the parents are healthy) then use the recessive setting. With “recessive homozygous” a homozygous variant an affected individual will be filtered out if and only if it is also present as a homozygous variant in an unaffected individual. With “recessive heterozygous” variants will only pass the filter if and only if they do not occur in an unaffected individual.
• If you are analyzing a disease where the phenotype seems to follow a dominant pattern of inheritance (typical scenario: around half of the offsprings are affected and one of the parents is affected, too), then use the dominant setting. A heterozygous variant in an affected will then pass the filter if and only if the variant has not been detected in the individuals that are assigned a not affected.

A usual scenario for will be a Trio analysis. In such a case you will have the variant data of the an affected child and the two parents. If you suspect a recessive disease, you will probably have to set the parents as unaffected and select “recessive”. In case you are looking for a dominant disease gene, either one of the parents is now affected, too. Or, if both parents are unaffected you will filter with the dominant setting for potential “de novo” mutations.

Good luck!