FiltersΒΆ

One of the key parts of the VCF processing is to filter quality calls. To do this we have created a flexible interface with variaety of filters avaialble:

  • qual_score - Filter records where QUAL score is below given threshold.
  • ad_ratio - Filter, defined by gatk, records where ratio of alt allele to sum of all alleles is below given fraction.
  • dp4_ratio - Similar to ad_ratio, but used in mpileup variant caller.
  • mq_score- Filter records that fall below specified MQ score (from _INFO_ field).
  • mq0_ratio - Filter, defined by gatk, records with MQ0 to DP ratio _above_ given threshold (both values are from _INFO_ field).
  • mq0f_ratio - Similar to the mq0_ratio, but used in mpileup variant caller.
  • qg_score - Filter records that fall below specified GQ score (from first sample).
  • min_depth - Filter records with mean depth below specified threshold (DP from sample field).
  • uncall_gt - Filter records with uncallable genotypes in VCF (GT is ./.).

All filters are applied for each position and those positions that pass ALL filters are kept as quality calls. Positions failing filter will be kept for future reference and creating fasta files, when needed. To specify filters to be used, simply list them as key:threshold pairs separated by comma(,). For filters that don’t require threshold, leave blank after ‘:’.