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

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

  X  N

POD ERRORS

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

Around line 43:

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