Get Allele specific copy number regions from WGS data using ASCAT?
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?
- I use
callto call snp from normal and tumour samples (I got tumour.vcf.gz and normal.vcf.gz)
- I use
eagleto do haplotype phasing on normal samples. (I got phased_normal.vcf.gz)
- extract same snps from normal and tumour sample fo downstream analysis.
- 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)
- 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?
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