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.

alleleCounter 4.1.0                                 May 2020                                    ALLELECOUNTER(1)