SNV¶
Identifies the nucleotides that overlap each position in the BAM file. All reads formed by a consensus less than the min_read_per_uid threshold are ignored. The type of each nucleotide at a position are assigned as follows:
- If a read is in duplex, its’ bases are assigned as duplex supported bases (D). Otherwise, they are assigned as singletons (S)
- For each stand (+ and -), if a consensus read was generated by at least strong_supported_base_threshold number of original reads, that base is assigned as a strong base (P and N). Otherwise, they are assigned as weak bases (p and n).
Parameters¶
-c –config: An optional configuration file which can specify any of the arguments described below -i –input: An input BAM containing collapsed reads. This file should be sorted by read position. -o –output: Path and name of an output VCF file containing candidate variants. -s –molecule_stats: Path and file name of an output tsv file containing position depth and molecule abundance information. -r –reference: Reference genome, in FASTA format. An index should be present in the same directory -tb –target_bed: A tab-delineated BED3 file in which to restrict variant calling. -vaft –variant_allele_fraction_threshold: Minimum variant allele fraction to call a variant on each strand. -mo –min_molecules: Total molecules (i.e. actual depth) required to call a variant at this position. This threshold should be adjusted if you are restriction to sites expected to be mutated. -mum –mutant_molecules: Minimum number of supporting molecules on both strands required to call a variant. -mrpu –min_reads_per_uid: Each consensus read must have been formed from at least this number of original reads to use this read in variant calling. -ssbt –strong_supported_base_threshold: Bases from a consensus read collapsed from at this number of original reads will be classified as a strong supporting base. -eds –enforce_dual_strand: Only variants with support on both the positive and negative strand will be called. -mq –min_qual: Bases from weak supporting molecules with less than this quality threshold will be treated as an “N”.