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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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purity=NA #47

Open stroke1989 opened 2 years ago

stroke1989 commented 2 years ago

Hi, After I got help from @dariober , I finally runned cnv_facets sucessfully.Appreciate! The output included a plot. I have several questions:

  1. why was the purity value NA in all of my sample? the following is one example from my cohort SCA_071 cnv

  2. How to determine heterozygous loss, homozygous deletion and loss of heterozygosity (LOH)? the following plot was intercepted from Ronglai Shen's article"FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing"

    facets article

I think that heterozygous loss means that the copy number decreased to 1, as the heterozygous loss event showed in the following plot, homozygous deletion means that copy number decreased to 0, however the following plot showed the total CN was 2 in loci where homozygous deletion events occurred.

heterozygous

can anyone help you interprete the plot generated by facets? Appreciate!

dariober commented 2 years ago

Hi- See if this helps https://github.com/mskcc/facets/issues/66

About the workings of facets package, you may get better answers by asking at https://github.com/mskcc/facets. My program, cnv_facets.R, is just a convenient wrapper around the facets package and snp-pileup and recently I haven't done much work on tumor-normal CNVs.