FACETS QC criteria

Starting with v2, the facets QC is versioned independent of the facets-preview. The version # is also logged (with column facets_qc_version) in facets_qc.txt and facets_review.manifest.

v1.0

TODO: add more details

1. Too low fraction of the genome diploidy (2-0 or 1-0)

2. dipLogR is too high (high homdels)

3. dipLogR is too low (high ploidy)

4. High ploidy filter

5. Hypersegmentation

6. Fragment size difference between T/N ("waterfall")

7. Invalid purity (purity = 0.3 or NA)

8. Large discordance in TCN between EM and CNCF

9. Too large fraction of genome subclonal

10. Discordance between integer copy number and logOR.

11. Contamination filter (homozygous SNPs)

v0.0

Initial version of facets QC.