Inherited from FixedResources
Inherited from ScheduleWithEmptyDefaultResources
Inherited from Configuration
Inherited from ConfigurationLike
Inherited from ProcessTask
Inherited from UnitTask
Inherited from Schedulable
Inherited from LazyLogging
Inherited from Task
Inherited from Dependable
Applies various filters and ensures proper VCF formatting for variants produced by FreeBayes.
This application of tools follows the procedure in bcbio's use of FreeBayes: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/variation/freebayes.py Briefly, does the following in order: - fix ambiguous (IUPAC) reference base calls - remove alternate alleles that are not called in any sample - split MNP variants into multiple records - updates AC and NS - sort records using a fixed length window - standardizes the representation of variants using parsimony and left-alignment relative to the reference genome* - remove both duplicate and reference alternate alleles
* See: http://genome.sph.umich.edu/wiki/Variant_Normalization
* Tool Requirements: - vcflib (https://github.com/vcflib/vcflib - vt (https://github.com/atks/vt) - bcftools (https://samtools.github.io/bcftools/) - bgzip (https://github.com/samtools/htslib)
You can set the path to the various scripts and executables within the configuration, or make sure they are on your PATH.