---
name: "Sanger::CGP::AlleleCount::Genotype"
section: "3pm"
platform: "linux"
package: "liballelecount-perl"
version: "4.3.0-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Sanger::CGP::AlleleCount::Genotype"
---

# Sanger::CGP::AlleleCount::Genotype(3pm)

- new

  Null constructor

- configure

  Set up the object for the current analysis.

  ```
    $genotype->configure('my.bam', $min_pbq, $min_mapq [, $fasta])
  ```

- \_wrap\_c\_alleleCounter

  Generic function to generate allele counts from a chr\\tpos\\n formatted file (1-based) by calling the C version.

  Calling function should provided an intermediate path for the output if data needs reformatting for SNP6 style loci input files.

- get\_full\_snp6\_profile

  Writes tab seperated allelic counts and depth to specified FH Uses all snps defined in file used by ngs\_cn (format slightly different)

- get\_full\_loci\_profile

  Writes tab seperated allelic counts and depth to specified FH Uses all loci defined in specified file

- gender\_chk

  Writes the chromosome name for the Male sex chromosome as defined by loci file and 'Y/N' indicating presence of any of the SNPs.  E.g.

  ```
    chrX  Y
  ```

  or

  ```
    X  N
  ```

## POD ERRORS

Hey! **The above document had some coding errors, which are explained below:**

- Around line 43:

  '=item' outside of any '=over'

  \=over without closing =back