.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH ALLELECOUNTER "1" "May 2020" "alleleCounter 4.1.0" "User Commands"
.SH NAME
alleleCounter \- NGS copy number algorithms
.SH SYNOPSIS
.B alleleCounter
\fI\,-l loci_file.txt -b sample.bam -o output.txt \/\fR[\fI\,-m int\/\fR] [\fI\,-r ref.fa.fai\/\fR]
.SH 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).
.SH OPTIONS
.TP
\fB\-l\fR  \fB\-\-loci\-file\fR [file]
Path to loci file.
.TP
\fB\-b\fR  \fB\-\-hts\-file\fR [file]
Path to sample HTS file.
.TP
\fB\-o\fR  \fB\-\-output\-file\fR [file]
Path write output file.
.SS Optional
.TP
\fB\-r\fR  \fB\-\-ref\-file\fR [file]
Path to reference fasta index file.
NB. If cram format is supplied via \fB\-b\fR and the reference listed in the cram header
.IP
can't be found alleleCounter may fail to work correctly.
.TP
\fB\-m\fR  \fB\-\-min\-base\-qual\fR [int]
Minimum base quality [Default: 20].
.TP
\fB\-q\fR  \fB\-\-min\-map\-qual\fR [int]
Minimum mapping quality [Default: 35].
.TP
\fB\-c\fR  \fB\-\-contig\fR [string]
Limit calling to named contig.
.TP
\fB\-d\fR  \fB\-\-dense\-snps\fR
Improves performance where many positions are close together
.TP
\fB\-x\fR  \fB\-\-is\-10x\fR
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.
.IP
by iterating through bam file rather than using a 'fetch' approach.
.TP
\fB\-f\fR  \fB\-\-required\-flag\fR [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. \fB\-F\fR  \fB\-\-filtered\-flag\fR [int]       Flag value of reads to exclude in allele counting default: [3852].
.TP
\fB\-v\fR  \fB\-\-version\fR
Display version number.
.TP
\fB\-h\fR  \fB\-\-help\fR
Display this usage information.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.