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ALLELECOUNTER(1) User Commands ALLELECOUNTER(1)

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

Path to loci file.
Path to sample HTS file.
Path write output file.

Optional

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.
Minimum base quality [Default: 20].
Minimum mapping quality [Default: 35].
Limit calling to named contig.
Improves performance where many positions are close together
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.
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].
Display version number.
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.

May 2020 alleleCounter 4.1.0