Agile Variant Selector
Agile Variant Selector reads multiple VCF files or 'annotated VCF' like files and
identifies variants which occur at least n times in the data from affected individuals and discounts any variant that
appears in a normal individuals data set.
Note: The program does not take note of the read depth, allele/variant read depth ratio or genotype
of the variants. This could be done if you wanted but you'll have to ask for it.
Instructions:
- Place the data for the affected patients in an empty folder
- If you have data on unaffected individuals place that in a second empty folder.
- Enter the type of file you are using using the radio button options: Text files or VCF files.
- Select the folder(s) using the 'Affected' and 'Unaffected' buttons.
- Select the minimum number of occasions a variant must appear in the affected patients for it to be retained using the 'Minimum count' option.
- Press the 'Analyse' button and enter the name of the export file.
- The data will be exported in a similar format to the imported data. The start of each line will contain a series of columns containing 'Yes' or 'No' which indicates which files the variant was in. After that the base data for the variant is repeated (i.e. chromosome, sequence change, position, RS ID). This is followed by the read depth data for the variant in each of the files it was in. If the variant was not in a certain file these fields are left blank.