We are working on comparison between several callers and we have some questions regarding ploidy estimates. In FACETS output ploidy of the sample is 3. For other callers, example: GATK, ploidy is not set and we assume it is 2.
How to compare those results? Should we adjust results from FACETS to 3, meaning that result >3 would be gain, ==3 would be neutral, and <3 would be loss, or in which way to compare those results to other callers, for example GATK or FREEC?
Hi,
We are working on comparison between several callers and we have some questions regarding ploidy estimates. In FACETS output ploidy of the sample is 3. For other callers, example: GATK, ploidy is not set and we assume it is 2.
How to compare those results? Should we adjust results from FACETS to 3, meaning that result >3 would be gain, ==3 would be neutral, and <3 would be loss, or in which way to compare those results to other callers, for example GATK or FREEC?
Thank you in advance