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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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purity is NA and how to interpret the plot #178

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:

why was the purity value NA in all of my sample? the following is one example from my cohort 176418574-823921f4-1e68-412f-b234-99fcfcf6ebb0

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!

xiasijian commented 1 year ago

The question to me.

zxclovezby commented 11 months ago

The question to me.