ALLELECOUNTER

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.