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Sanger::CGP::AlleleCount::Genotype(3pm) User Contributed Perl Documentation Sanger::CGP::AlleleCount::Genotype(3pm)

Null constructor
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.

Writes tab seperated allelic counts and depth to specified FH Uses all snps defined in file used by ngs_cn (format slightly different)
Writes tab seperated allelic counts and depth to specified FH Uses all loci defined in specified file
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:

'=item' outside of any '=over'

=over without closing =back

2021-10-07 perl v5.32.1