NAME

       alleleCounter - NGS copy number algorithms

SYNOPSIS

       alleleCounter -l loci_file.txt -b sample.bam -o output.txt [-m int] [-r ref.fa.fai]

DESCRIPTION

       Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file
       and generates a count of coverage of each allele [ACGT] at that location (given any filter
       settings).

OPTIONS

       -l  --loci-file [file]
              Path to loci file.

       -b  --hts-file [file]
              Path to sample HTS file.

       -o  --output-file [file]
              Path write output file.

   Optional
       -r  --ref-file [file]
              Path  to reference fasta index file.  NB. If cram format is supplied via -b and the
              reference listed in the cram header

              can't be found alleleCounter may fail to work correctly.

       -m  --min-base-qual [int]
              Minimum base quality [Default: 20].

       -q  --min-map-qual [int]
              Minimum mapping quality [Default: 35].

       -c  --contig [string]
              Limit calling to named contig.

       -d  --dense-snps
              Improves performance where many positions are close together

       -x  --is-10x
              Enables 10X processing mode.  In this mode the HTS input file must be a  cellranger
              produced  BAM  file.  Allele counts are then given on a per-cellular barcode basis,
              with each count representing the consensus base for that UMI.

              by iterating through bam file rather than using a 'fetch' approach.

       -f  --required-flag [int]
              Flag value of reads to retain  in  allele  counting  default:  [3].   N.B.  if  the
              proper-pair  flag  is are selected, alleleCounter will assume paired-end and filter
              out any proper-pair flagged reads not in F/R orientation. -F  --filtered-flag [int]
              Flag value of reads to exclude in allele counting default: [3852].

       -v  --version
              Display version number.

       -h  --help
              Display this usage information.

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.