usage: smCounter.v2.4.py [-h] [--runPath RUNPATH] [--bedName BEDNAME]
[--bamName BAMNAME] [--prefix PREFIX] [--nCPU NCPU]
[--minBQ MINBQ] [--minMQ MINMQ] [--hpLen HPLEN]
[--mismatchThr MISMATCHTHR] [--primerDist PRIMERDIST]
[--mtThreshold MTTHRESHOLD] [--rpb RPB] [--isRna]
[--primerSide PRIMERSIDE] [--minAltUMI MINALTUMI]
[--maxAltAllele MAXALTALLELE] [--refGenome REFGENOME]
[--repBed REPBED] [--srBed SRBED]
Variant calling using molecular barcodes
optional arguments:
-h, --help show this help message and exit
--runPath RUNPATH path to working directory
--bedName BEDNAME BED file
--bamName BAMNAME BAM file
--prefix PREFIX file name prefix
--nCPU NCPU number of CPU to use in parallel
--minBQ MINBQ minimum base quality allowed for analysis
--minMQ MINMQ minimum mapping quality allowed for analysis
--hpLen HPLEN Minimum length for homopolymers
--mismatchThr MISMATCHTHR
average number of mismatches per 100 bases allowed
--primerDist PRIMERDIST
filter variants that are within X bases to primer
--mtThreshold MTTHRESHOLD
threshold on read proportion to determine MT level
consensus
--rpb RPB mean read pairs per UMI; default at 0 and will be
calculated
--isRna RNAseq varinat calling only; default is DNAseq
--primerSide PRIMERSIDE
read end that includes the primer; default is 1
--minAltUMI MINALTUMI
minimum requirement of ALT UMIs; default is 3
--maxAltAllele MAXALTALLELE
maximum ALT alleles that meet minAltUMI to be
reported; default is 2 (tri-allelic variants)
--refGenome REFGENOME
Path to the reference fasta file
--repBed REPBED Path to the simpleRepeat bed file
--srBed SRBED Path to the full repeat bed file
