usage: run.py [-h] [--runPath RUNPATH] [--bedTarget BEDTARGET]
[--bamFile BAMFILE] [--outPrefix OUTPREFIX] [--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] [--ds DS] [--bamType BAMTYPE]
[--inputVCF INPUTVCF]
smCounter2: variant calling using Unique Molecular Identifiers
optional arguments:
-h, --help show this help message and exit
--runPath RUNPATH path to working directory
--bedTarget BEDTARGET
BED file
--bamFile BAMFILE BAM file
--outPrefix OUTPREFIX
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. If the
bam is tagged with its mate's mapq, then the minimum
of the R1 and R2 mapq will be used for comparison, if
not each read is compared independently.
--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
--ds DS down sample if number of UMIs greater than this value
(for RNA only)
--bamType BAMTYPE raw (default): raw BAM file with UMIs; consensus:
consensused BAM file
--inputVCF INPUTVCF optional input VCF file
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