NAME¶

Sanger::CGP::AlleleCount::Genotype - Perl interface to alleleCounter

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 separated 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 separated 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