Obtain BAF and LogR from the Germline allele counts

Source: R/prepare_wgs_germline.R

Function to generate BAF and LogR files based on allele counts of the Germline. It also generates the input data required by the following 'germline_reconstruct_normal' function.

germline_baf_logR(GERMLINENAME, g1000alleles.prefix, chrom_names)

Arguments

GERMLINENAME

The germline name used for Battenberg (i.e. the Germline BAM file name without the '.bam' extension).

g1000alleles.prefix

Prefix to where 1000 Genomes allele files can be found.

chrom_names

A vector with allowed chromosome names.

Author

Naser Ansari-Pour (BDI, Oxford)