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

Run Using

produse call


python /path/to/ProDuSe/ProDuSe/


-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