vcffilter: Filter VCF files for exome sequencing experiments

vcffilter allows you to filter VCF files to prioritize variants in sequencing studies.

vcffilter requires python 2.7

Info field filters

the --info_filter flag allows you to filter based on the contents of the INFO field. To avoid problems with shells, the symbols >, >=, <, <=, ==, != are replaced with gt, gte, lt, lte, eq, and neq, respecitively. INFO flags can be filtered with --info_filter <FLAG> is set and --info_filter <FLAG> not set. You can also filter strings with contains and ncontains.

Examples:

• --info_filter CG gt 2: Only return records with GERP scores greater than 2
• --info_filter DB not set: Return variants not in dbSNP
• --info_filter PH contains damaging: Only return records predicted damaging by polyphen

Model-based filtering

You can filter for variants matching a Mendelian genetic model with the --model dom and --model rec flags. --model dom only returns genotypes that match a dominant model, namely those where each individual has a minor allele. --model rec only returns genotypes that match a recessive model, that is those that match the follwing criteria: 1) everyone has two minor alleles and 2) everyone is homozygous.

Other filters

• --region 5 10000 20000 filters only variants within Chromosome 5, from 10000 to 20000bp
• --geno .5 requires that at least half of individuals must have a genotype called
• --no-qc doesn't add the filter (on by default) that the FILTER column equals 'PASS'
• --qual 25 only returns variants with QUAL field > 25

Filter priority

Filters are applied in the following order:

1. Region
2. Minimum quality
3. FILTER = 'PASS'
4. Minimum call rate
5. Info filters, in order they were specified.
6. Mendelian Model filters