Sliding-window indel correction
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
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