allele specific copy number

[tan...@gmail.com]

Dear all,

I would appreciate having your help on the following : I would like to use a software that is called scarHRD to measure the degree of homologous recombination deficiency (HRD) in cancer cells. The link to the scarHRD package is : https://github.com/sztup/scarHRD

ScarHRD accepts as input either the standard sequenza files that predict the copy number alterations (CNA) and loss-of-heterozygosity (LOH) on normal-tumor pairs, and  have the format :

chromosome

position

base.ref

depth.normal

depth.tumor

depth.ratio

Af (A allele frequency)

Bf (B allele frequency)

zygosity.normal

GC.percent

good.reads

AB.normal

AB.tumor

tumor.strand

into a simpler format that is :

Chromosome

Start_position

End_position

total_cn (total copy number)

A_cn (copy number of allele A)

B_cn (copy number of allele B)

In other words, the question is how do I transform

Af (A allele frequency) ; Bf (B allele frequency) ; depth_tumor, dept_normal into

copy_number_of_alelle_A and copy_number_of_allele_B ?

Thanks a lot,

Bogdan