---
name: "alleleCounter"
section: "1"
platform: "linux"
package: "allelecount"
version: "4.3.0-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alleleCounter"
---

# alleleCounter(1)

NGS copy number algorithms

## 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.