Call¶
Identifies all possible positions which support an alternate allele (no matter how weakly) across the entire capture space. These variants are then filtered using a random forest filter, based upon numerous characteristics
Parameters¶
-c –config: An optional configuration file which can specify any of the arguments described below -i –input: An input BAM containing collapsed (and ideally clipped) reads. This file must be sorted by position. -o –output: Output VCF file containing filtered variants -u, –unfilted: Output VCF file containing ALL possible variants -r –reference: Reference genome, in FASTA format. A reference index should be present in the same directory -t –target_bed: A BED3 file specifying a capture space to restrict variant calling -f, –filter: A piclke containing a tranined Random Forest Classifier