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 standard sequenza files that predict the copy number alterations (CNA) and loss-of-heterozygosity (LOH) on normal-tumor pairs, and that 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
