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:

  1. If a read is in duplex, its’ bases are assigned as duplex supported bases (D). Otherwise, they are assigned as singletons (S)
  2. 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).

Run Using

produse snv

or

python /path/to/ProDuSe/ProDuSe/snv.py

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”.