Get Allele specific copy number regions from WGS data using ASCAT?

Question

[xiaoguang]

Hi,

I have some paired samples(normal vs. tumour) and want to do allele specific CNA analysis. can you help me to check if I use the right pipeline?

1. I use bcftools mpileup and call to call snp from normal and tumour samples (I got tumour.vcf.gz and normal.vcf.gz)
2. I use eagle to do haplotype phasing on normal samples. (I got phased_normal.vcf.gz)
3. extract same snps from normal and tumour sample fo downstream analysis.
4. calculate BAF and logRR (BAF = haplotype_2_counts/(haplotype_1_counts+haplotype_2_counts), logR_tumour= tumour_total_count/normal_total_count, logR_normal=0)
5. running ASCAT pipiline

   library(ASCAT)
   ascat.bc = ascat.loadData("ascat/tumour.logR.txt","ascat/tumour.baf.txt",
                          "ascat/normal.logR.txt", "ascat/normal.baf.txt",chrs = c(1:22))
   ascat.plotRawData(ascat.bc)
   ascat.bc = ascat.aspcf(ascat.bc)
   ascat.plotSegmentedData(ascat.bc)
   ascat.output = ascat.runAscat(ascat.bc,gamma=1)
   

   I also try ASCATngs pipeline and finally I got different result segments from this two method. But I don't know which step I used was wrong?