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Published 20 hours ago • verified publisher icon mskcc

purity is NA and how to interpret the plot

Open stroke1989 opened this issue 2 years ago • 2 comments

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!

stroke1989 avatar Jun 30 '22 07:06 stroke1989

The question to me.

xiasijian avatar Dec 12 '22 00:12 xiasijian

The question to me.

zxclovezby avatar Dec 20 '23 02:12 zxclovezby