Filter Variants

Filter variants based on some annotation from the INFO field of a vcf file.

Examples

genmod -v filter examples/test_vcf_annotated.vcf -a 1000G_freq -t 0.01

This command will skip all variants that have a 1000G_freq < 0.01. By default all variants that lack 1000G_freq will be kept, this can be modified by the -d/--discard flag.

genmod -v filter examples/test_vcf_annotated.vcf -a CADD -t 7 --greater --discard

Here we will filter out all variants that have annotation CADD less than 7 and all variants that miss the CADD flag.

Command

$ genmod filter --help
Usage: genmod filter [OPTIONS] <vcf_file> or -

  Filter vcf variants.

  Filter variants based on their annotation

Options:
  -a, --annotation TEXT   Specify the info annotation to search for. Default
                          1000GAF
  -t, --threshold FLOAT   Threshold for filter variants. Default 0.05
  -d, --discard           If variants without the annotation should be
                          discarded
  -g, --greater           If greater than threshold should be used instead of
                          less thatn threshold.
  -s, --silent            Do not print the variants.
  -o, --outfile FILENAME  Specify the path to a file where results should be
                          stored.
  --help                  Show this message and exit.