areebapatel / qiaseq-smcounter-v2

qiaseq-smcounter-v2

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