Windel
Sliding-window INDEL correction
NAME
windel.py - Performs windowed indel analysis in a multiprocessing fashion.
SYNOPSIS
windel.py REFERENCEFILE ALIGNMENTFILE OUTFILE <flags>
DESCRIPTION
Performs windowed indel analysis in a multiprocessing fashion.
POSITIONAL ARGUMENTS
REFERENCEFILE
path to reference fasta file
ALIGNMENTFILE
path to alignment file (bam/sam)
OUTFILE
path to output file (csv)
FLAGS
--fasta_out=FASTA_OUT
Optional path to corrected fasta output (default None).
--prop_thresh=PROP_THRESH
threshold for the proportion of windowed reads having an indel at a position for an edit to be made (default 0.9)
--window=WINDOW
width of window to use, must be odd (default 11)
--processes=PROCESSES
number of processes to spawn (default is the number of cpus)
NOTES
You can also use flags syntax for POSITIONAL ARGUMENTS